Bookends Changelog

What's new in Bookends 15.0.1

Apr 9, 2024

Halt PDF downloads when importing many references at once (batch downloading)
The download progress window now has a Stop button in additon to Skip. This may be useful if, for example, Internet access is slow or you have mistakenly triggered the search and download process for many references at once.
Updated Journal Glossary
The Journal Glossary window is no longer modal and follows the conventions of nomal document windows, including Command-S to save and Command-W to close. Use a right-click contextual menu to remove a journal. Clicking the plus button to add a journal creates an empty row for you to fill. Move from column to column by pressing Tab (forward) or Shift-Tab (backward).
Edits to a journal glossary will take effect immediately
Previously this required an app relaunch.
Search all fields or individual database fields (e.g. Authors, Title, etc.) while using Floating Citations
Click on the search field magnifying glass to select a specific field.
A right-click on controls in the library window will open the appropriate contextual menu even when it is in the background
Change the font size of the Summary pane via a right-click contextual menu
The same size will be used for notecards.
Bookends will not let you create a new library in a file sync folder (e.g. Dropbox, iCloud Drive, etc.)
Such services can corrupt databases. Synchronization should only be done by Bookends cloud sync, which syncs the data, not the file.
More information in provided when checking for updates
Cosmetic improvements
Fixes:
Fixed a bug where PDFs imported from the watch folder weren't renamed if they were attached to an existing reference.
Fixed a bug in the Journal Glossary window were Edit -> Paste did not insert text into the search field or list cells.
Fixed a bug when attaching multiple PDFs at once where a PDF could be attached to the wrong reference.
A question mark at the end of an imported title will be preserved.
Removed mentions of the Web of Science from the UI.
Fixed a bug when using a CSL style where only the first initial was output when the authors name contained two or more initials in a row.

New in Bookends 15.0.0 (Mar 11, 2024)

Citation Style Language (CSL) style support:
CSL styles are analogous to Bookends formats — templates that describe how reference metadata should appear in citations and bibliographies. Individual styles are available from the CSL project, Zotero.org, and other online sources. Their content cannot be viewed or edited in Bookends, but there are apps and online sites where this can be done. As a rule, we recommend that you use Bookends native formats rather than CSL styles. Formats are faster, easily and endlessly configurable, and have many useful capabilities unavailable in CSL styles. CSL styles, on the other hand, are not easily created or edited, may yield imprecise results because not all Bookends and CSL fields are equivalent, and have no Bookends-specific functionality. Having said that, if you need a format that isn't included with Bookends and can't find another that fulfills the bibliographic requirements and don't want to create one yourself, you may find a CSL style that meets your needs. There are some Bookends-specific features for which CSL styles cannot be used: renaming attachments, generating citekeys, and creating a format catalog.
Download and install CSL styles within Bookends:
Use Biblio -> Find & Import CSL Style to download CSL styles from the Zotero Style Repository. Style files will be imported into the Custom Formats folder and enabled for use. You can install and enable CSL style files you already have by dropping them on the library window. Alternatively, you can move them in the Finder to the Custom Formats folder and enable them in the Formats Manager.
Upgraded database engine:
Libraries created or opened in Bookends 15 or later cannot be opened by older versions. When you open a library made with an older version, Bookends will offer to create a backward-compatible copy with the same name plus the word "previous", then proceed to update the database and open the library. The backward-compatible copy will be created in the same folder as the library.
Improved PDF annotations:
A sixth color option has been added, and underlines will have the color that is selected in the annotation popover. If "no color" is selected, the underline will be red.
Customize the punctuation that separates multiple grouped citations in the final scanned result
In addition to the factory-supplied citation separators available via a pop-up menu, you can use any combination of punctuation and spaces you indicate in the format's Citation Options -> Common Settings tab. This applies to author-date and custom citations.
Improved journal glossaries:
The UI for entered and editing journals has been updated, and the speed of journal name retrieval is much faster.
Added a new journal glossary: Medline:
This glossary, which contains over 19,000 journals, replaces the Concise Medline glossary, which contained only 830. If you have been using the factory default Concise Medline glossary, please reset the selection in Windows -> Journal Glossaries to Medline.gloss.
The database .journal file is now kept in Application Support -> Bookends:
This file, which records database transactions and is used to restore them in case of a crash, was previously created in the same folder as the library, which caused clutter and confusion as to its purpose.
The Web Of Science direct search filter has been removed:
Use Bookends Browser to search and obtain references instead.
Other:
The height of the Abstract viewing area in the Citation Inspectors and the My Publications window is adjustable
The About Bookends window has been refreshed and contains more information
If a Crossref DOI search returns an article number instead of page number, the article number will be imported into the pages field
Fixes:
Multiple temp citations in a group will be separated by semicolons when created for Mellel, regardless of how this is specified in Settings.
Fixed a renaming bug when adding a format by drag and drop, the format already exists, and Keep Both is pressed.
Bookends will not strip a trailing hyphen from DOIs and URLs on import.
Fixed an infinite error loop that could occur when viewing the note stream of a corrupted PDF.

New in Bookends 14.1.6 (Jan 8, 2023)

Introducing deep PDF links. You can create a hypertext link to any PDF text or annotation and insert in into 3rd party applications like Scrivener, DevonTHINK, and Obsidian, or into Bookends reference fields themselves (e.g. Notes). Deep links to selected text are created in the annotation popover window (Copy Link). You can create links to annotations in two ways: (1) right click on the annotation, select Copy Link from the contextual menu, and paste it into a compatible app, or (2) Command-drag the annotation to a window in a compatible app. Annotation links work with Highlight, Underline, Note, and Comment annotations created in Bookends or any other PDFKit-compliant application. If the corresponding Bookends library is open when the link is clicked, you will be taken to the reference/PDF and the linked text or annotation selected. In the copy or drag Bookends will also include a markdown link in the form [descriptive text](link). This allows you to use links with apps such as Obsidian and Bear, which do not recognize native links. You can rename the PDF without breaking the link. However, if you move a linked PDF Note or Comment on the page Bookends won't be able to locate it. In this case Bookends will still open the PDF of the linked reference and take you to the correct page, it just won't select the annotation. Note that to paste a live link into a reference field, it must support styled text and you must perform a plain Paste, not Paste And Match Style. If you set Command-V to use Paste And Match Style in Preferences, paste the link with Edit -> Paste or the keyboard shortcut Shift-Option-Command-V.
Compatible with macOS Ventura 13.2 (a)
Clicking on an underline annotation will select the corresponding notecard if the note stream is open and the option to show PDF annotations is active
Swap two PDF tabs by holding down the Command key and dragging and dropping one tab onto the other
Added the option to remove duplicates from selected references (Refs -> Remove Duplicates). Previously Bookends would only search the entire library for duplicates.
Preferences list containing field labels (Refs tab) has a new column that displays the default (original) values. This is useful if you have renamed and/or rearranged labels and need to know what metadata is intended for the corresponding field. You can reset a label to its default with a right-click, or edit it manually.
Updated import of nonstandard EndNote XML files exported from Mendeley
Bug fixes:
References in the Trash will not be used when creating or syncing a linked BibTeX file. Fixed a bug where the first column in the reference list couldn't be sorted by clicking on the header. Fixed a bug where the middle pane's width couldn't be changed in widescreen view. Fixed a bug where the library window panes sometimes didn't update when a reference was selected. Fixed several bugs in how the edit pane Notes field is displayed when switching between Light and Dark Mode. Fixed a bug where edits made in an edit field would be lost if you immediately right-click on the field and choose Change Case. Fixed a bug where Bookends didn't properly account for references in the Trash, resulting in a spurious warning that some references didn't have citekeys when creating a synced BibTeX file. Fixed a bug where opening a PDF in LiquidText would also launch Highlights. Fixed a bug where a short title created with a right-click on the title field could be shown in gray. Fixed a bug where trying to remove a reference from a group could fail when the browser pane was open.

New in Bookends 14.1.5 (Dec 4, 2022)

Improvements in library window reference list sort behavior. The sort column and direction (ascending vs. descending) is saved independently for each library when it is closed and restored when it is opened. Previously, when a library was opened an ascending sort was performed on the first column.
Add and/or remove reference list columns in the UI. Right-clicking on a list column header brings up a contextual menu that lists all of the possible options (e.g. Authors, Title, Added, Attachments, etc.) that can be displayed, with those currently showing being checked. Select a checked value to remove it from display, select an unchecked value to add it as a column immediately preceding the header that was clicked on. The minimum number of columns is 3, the maximum is 10. The options to add or remove columns still exist in Preference, this new feature is a convenient shortcut.
Scroll PDF tabs horizontally. When there are too many tabs to view all at once, place the mouse pointer over the PDF toolbar or the "no attachment" image, if showing, and swipe left or right to scroll horizontally. This works with track pads and the Apple Magic Mouse.
When a PDF tab is selected using a right-click contextual menu the PDF tabs will scroll, if necessary, so that it is visible
PDF highlight and underline page numbers are now shown in the note stream
The PDF Action pop-up option Show Annotation Modification Date in Notecards now applies to highlights and underlines
Previously it applied only to notes. Be aware that modification date for some annotations is not available in older versions of macOS.
Sort notecards by page number. Right-click on the note stream to open contextual that lets you sort notecards from the Notes field (not PDF annotations, which are already sorted by page number) if they have a page number indicated by "@". Notecards without page numbers will be left in their original position. This contextual menu option will appear if the note stream contains two or more notecards created from Notes.
Removed Copy As Hypertext Link from the note stream contextual menu
This option was misleading because it copied a link to the reference, not to selected the notecard. There is already an option to copy the link to the reference in the Edit menu.
Quickly navigate between pages you've viewed in Bookends Browser. Click and hold or right-click on the forward/back navigation buttons to open a contextual menu that will let you quickly go to web pages visited in the current session.
Improved detection of DOIs in PDFs from PNAS
Updated how automatic PDF downloads from eLife are handled to deal with changes made by the publisher
When formatting, the BibTeX Markup setting will only be applied if the format name contains the word BibTeX. If it does not, the reference will be output as styled text. This means you can switch between conventional formats and BibTeX.fmt without having to explicitly adjust the output style.
BibTeX keys are now referred to as Citekeys throughout the UI
When formatting with BibTeX Markup, superscripts will be indicated by textsuperscript{}
When you right-click on the note stream and Copy Notecard and Citation, any headers, page numbers, and tags will be removed
Added LiquidText as an optional PDF reader
Bug fixes:
Fixed a cosmetic bug in the widescreen view when changing the groups pane width while the the formatted reference was being displayed. Fixed a bug where an error could occur when switching between the library window and a standalone reference window when the Formats Manager was open. Updated Copy Citation from the floating citation window to work with Scapple. Fixed a bug where PDFs automatically fetched from PubMed Central were downloaded twice. Fixed a bug in the note stream where moving a PDF annotation notecard into the list of database field notecards could cause notecards to merge. BibTeX bracketing of acronyms will no longer bracket runs of capital letters that occur inside a string. Fixed a bug where having a space in the PMID field could cause an error when using it to search for the PDF.

New in Bookends 14.1.4 (Nov 7, 2022)

Minor adjustments for macOS macOS 16 Ventura
Automatic downloading works with many more PDFs. If you attempt to download a PDF whose URL can't be resolved or is behind an unaccessible paywall to a reference that has a DOI, Bookends will query Unpaywall (https://unpaywall.org) to obtain it from a repository on which it has been legally uploaded. You can learn more about Unpaywall, which keeps track of repositories containing millions of articles from thousands of publishers, in their FAQ: https://unpaywall.org/faq.
Added more publications as targets for automatic PDF downloading
If an online search finds references you already have (e.g. they are highlighted in yellow), right-click to select and display them in your library window
When importing a duplicate reference when attaching a PDF, Bookends will offer to show you the existing copy even when it's in the trash
The online search display of references will use the list text font and size selected in preferences
Copy live hypertext links to folders in the groups pane
Send formatted references to the bibliography window
The pop-up menu listing attachments will be enabled even if there is only one
Previously it would be disabled and you couldn't see the entire name if it exceeded the width of the menu.
Bug fixes:
Fixed an error that occurred when using the PDF action pop-up in a standalone editing window. Fixed an error that occurred with the Summary view. Fixed a bug that prevented hanging indents from showing in the bibliography window. Fixed a bug where the right reference might not be selected when using a right-click -> Show This Reference In Library in the Online Search window. The Summary pane updates immediately when its font size is changed in preferences. Fixed a cosmetic bug where attachment names shown in the reference list weren't immediately updated when renamed. Fixed a problem in the registration code window where the dates weren't parsed as intended for some non-English System languages. Fixed a bug where the year was incorrect in exported XML when the Date field contained styled text. Fixed a bug in Get DOI where the search failed when the title or journal name contained characters that should be escaped. Fixed a bug where the setting to not include the PDF pathname with extracted annotations was ignored. Fixed a bug where showing edit pane hints was turn on by default when a new library was made.

New in Bookends 14.1.3 (Oct 10, 2022)

Much improved extraction of PDF annotations. The ability of Bookends to extract and export PDF annotations has been rewritten from the ground up, and is now reference- rather than PDF-centric. This means that the annotations "know" which reference the PDF is attached to. Now each annotation block, which contains the annotations from all PDFs attached to a reference, is headed by information about the reference. This information is created using the default format (Biblio -> Default Format) and style (e.g., Styled Text, Plain Text, BibTeX Markup, etc.). This means you can include any information the formatter can access, including the unique ID, linked references, etc. Extracted highlights can be shown in the same color as in the PDF (light mode only). Annotations are output to a new Annotation Window, which gives you instant access to your annotations while working in Bookends itself. Search the contents of the annotation window using Command-F. You can copy and paste the contents into other applications, or save the contents to disk using File -> Save PDF Annotations.
Improved file downloading in Bookends Browser. Bookends Browser now works for download links for many file types, not just PDFs. It's intelligent, meaning that Bookends will offer to attach downloaded PDFs and Word files (as well as some other document types), whereas .zip files will be directly downloaded to your Downloads folder. How files are handled depends upon the MIME type assigned by the server. Requires macOS Big Sur 11.3 or later.
Text styles are now included when you drag notecards to another app with the Option key held down
Color label pop-up menus now show the color along with the assigned text
More graceful handling of the Inspector if the user-selected format for the display of references is deleted
HTML markup for text styles will be removed from PubMed abstracts, if present
Changes to the content obtained when you copy or drag a notecard. When you drag a notecard with the Option key held down or copy it to the clipboard, all text and formatting cues (e.g. # for header, @ for page, etc.) will included. This makes it possible to manipulate the header, tags, quotes, etc. with a macro or script in the receiving app. Any styles you may have applied will be preserved. To be compatible with markdown, when Bookends adds a # to a new notecard to indicate the line is a header it will be followed by a space.
Minor cosmetic enhancement to the standalone Term List window
The pop-up menu listing attachments will be enabled even if there is only one
Previously it would be disabled and you couldn't see the entire name if it exceeded the width of the menu.
Bug fixes:
Fixed an error that occurred when using the PDF action pop-up in a standalone editing window. Fixed an error that occurred with the Summary view. Fixed a bug that prevented hanging indents from showing in the bibliography window. Fixed a bug where the right reference might not be selected when using a right-click -> Show This Reference In Library in the Online Search window. The Summary pane updates immediately when its font size is changed in preferences. Fixed a cosmetic bug where attachment names shown in the reference list weren't immediately updated when renamed. Fixed a problem in the registration code window where the dates weren't parsed as intended for some non-English System languages. Fixed a bug where the year was incorrect in exported XML when the Date field contained styled text. Fixed a bug in Get DOI where the search failed when the title or journal name contained characters that should be escaped. Fixed a bug where the setting to not include the PDF pathname with annotations was ignored.

New in Bookends 14.1.2 (Sep 4, 2022)

New in Bookends 14.1.1 (Aug 8, 2022)

Refreshed Bookends app icon
New Trash group. When you delete a reference it is placed in the trash rather than being deleted from the database. If you drag a reference to the trash or press Command-Delete you will bypass the warning message. You can restore references from the trash or permanently delete them from the library. References in the trash can still be used, with a few exceptions: Live Search will find references in the trash only when the trash group is selected and scanning won't find matches with references in the trash. In addition, you can't extend group selections that include the trash, meaning that it can't participate in virtual groups. If you're syncing with Bookends for iOS, trash will sync automatically for cloud sync, but Wi-Fi sync requires version 3.7.6 or later.
Formatted reference examples include secondary citations. Custom citation formats can output different results depending on whether the reference is cited for the first time or a subsequent time. For such formats, the examples in the Format Manager and in the library window formatted reference pane include the first (1°) and secondary (2°) forms. If the format has no entry for subsequent citations, these will be identical.
Use Copy Formatted for citations. Previously Copy Formatted only allowed you to copy the formatted bibliography output.
Perform smart change text case operations in the edit pane. Right-click on a field in the edit pane and select Change Case. The options are Sentence case, Title case, Uppercase, and Lowercase. Unlike the now-removed Transformations menu options, these operations leave any text styles intact and honor the words entered in preferences that are to be excepted (e.g., articles and proper nouns). This is identical to the Global Change-> Change Case function but much more convenient if you simply want to change one or a few references.
Use Delete (the key or the menu options) to move references in smart groups or the Recently Viewed group to the trash
Improved display of the groups you have created
Improved automatic detection and correction of some database problems
If a library is stored on a service like Dropbox, iCloud Drive, etc. you will receive a warning notification when it is opened. Databases are prone to corruption when entire files are synced. If you receive this warning, move the library file out of file sync folder and use Bookends cloud sync instead. It is much faster, more robust, and can serve as a backup mechanism if the library file itself becomes damaged.
The option to exclude leading parts of authors names when sorting will honor smart apostrophes, for example d’
Improved compatibility with PopClip. The PDF annotation popover window should remain open when PopClip is active.
Bug fixes:
Fixed a problem that prevented the color pickers in preferences from working. Fixed a bug where renaming corrupted a smart group. Fixed a bug where a new reference wasn't automatically added to the selected static group. Fixed a bug where the standalone edit window didn't update its contents when another reference was opened for editing. Fixed a bug where the standalone edit window title was incorrect when first opened. Fixed a bug where the wrong reference could be shown in the edit pane when the library was opened or a group changed. Fixed a bug that prevented some information found with an online search from being imported. Fixed an error caused by editing the "Replace repeated authors with" in a format. Fixed a bug where compound words in the author sort ignore list weren't used. Fixed a bug where new annotations weren't extracted unless the PDF had been saved. Fixed a bug where the subfolder selection pop-up menu wasn't updated immediately after creating a new subfolder. Fixed a problem where a terminal period before Cited Pages wasn't removed if it was followed by a Return. Fixed a bug where a right-click on a keyword tag incorrectly offered to add it to the stop list. Fixed a problem with Mellel verification of citations containing both literal text and a metacharacter.

New in Bookends 14.1.0 (Jul 3, 2022)

Completed a multi-year effort to refactor and modernize large amounts of the code base
New UI for searching Notes. When the edit pane Notes tab is showing, use Refs -> Find -> In Notes (Command-F) to bring up a search bar with an option to replace text as well.
Search Semantic Scholar. Semantic Scholar is a research discovery resource that covers over 200 million papers in all fields of science. Its strength is that it uses a variety of AI-driven tools to return highly relevant results. Its limitations are that it doesn't allow boolean searches, doesn't search behind paywalls, and doesn't return volume or page numbers. It does, however, provide abstracts and information about the number of citations a paper has received.
Smart SQL groups can be duplicated. Available with a right-click on the group or a click on the Action pop-up menu.
Click and hold or right-click on the Bookends icon in the dock to select from a list of recently opened libraries. Bookends must be running at the time.
Import filter tags can contain commas. Commas are used to separate multiple tags that map to the same field. Previously, you therefore couldn't import metadata whose tag contained commas. Now you can do that by escaping the comma in the import filter like this: , . Thus, the tag "Abstract, Summary" in the text could be imported with this import filter tag: "Abstract, Summary" (without the quote marks). Fixed an error in logic in the restore default font and styles function.
Most contextual menu options in the Attachment Inspector will operate on multiple attachments at once. The exception is Rename Attachment, which works with the first selected attachment.
Added more group pane Action pop-up menu options
Improved instructions for file sharing in the dialog the participant sees when accepting a share invitation
Improvements in the Autocomplete Paper dialog UI
Updated the notification subsystem to work more reliably with macOS 12 Monterey and later
In the Online Search window, changing the site to search clears the results of a previous search
Removed Substitutions and Transformations from the Edit menu
Global Change -> Restore Default Font and Style is much faster
The process by which Bookends determines if a reference field contains styled text has been improved
Hypertext links to other apps invoked with a right-click now work in all user-defined fields
Previously they only worked in fields up to User4.
Bug fixes:
Fixed a bug in the ! formatting directive that outputs the library name. Fixed a bug where the field in which a notecard was being edited remained visible after the right pane was closed. Fixed a bug in Autofill From Internet where some DOIs weren't found on PubMed. Fixed a bug where the Notes field hint text itself could be saved to the database. Fixed a bug in the Online Search recent searches pop-up menu. Fixed a bug in the where the edit pane wasn't updated correctly when references were imported. Fixed a bug where the edit pane fields weren't resized properly when the library was opened. Fixed a bug in which the a reference field text style could become "stuck" when switching between references.

New in Bookends 14.0.9 (Jun 7, 2022)

Color labels for groups and folders. Groups and folders can be assigned a color defined in Preferences (Lists tab). Select a group color from a right-click contextual menu, the action pop-up menu beneath the groups pane, or the keyboard shortcut Control-Command-# (the number of the color is defined in the preferences Lists tab). You can only assign colors to groups and folders you create; the color of default groups (All, Hits, Attachments, and Recently Viewed) can't be modified .
Ignore citation delimiter metacharacter. When the open citation delimiter, typically a curly bracket, is immediately followed by a tilde (~), Bookends will ignore it during a scan. This is useful if you need to use the citation delimiter in another context, such as a mathematical formula, and don't want Bookends to mistakenly think it is the beginning of a temporary citation. When ready to submit the manuscript, do a search/replace in your word processor and replace the open delimiter plus ~ with the open delimiter (for example, replace {~ with { ).
Perform a live search for a unique ID by preceding it with the # character (e.g. #43237). You can already select Unique ID as a field to search in using the live search field pop-up menu; this is another way to do so that is arguably more convenient.
The library name output by the formatter will no longer include the file extension, .bdb
A colon will be used in place of an underscore before the unique ID when generating a citekey as Author + Year + UniqueID
If a file in the destination folder has the same name as an exported attachment, Bookends will move it to the Trash and then proceed with the export
Small UI tweaks. Updated Help menu wording. The right-click contextual menu for references in static group reads "Remove From Group" instead of "Delete". Improved display of edit pane when no reference is selected.
The note steam will scroll to a newly-imported notecard
Added a warning that importing from Papers 3 can't be done when running a macOS version later than Big Sur 11.2
Bookends will import issue numbers exported from Mendeley as EndNote XML.
Right-clicking on empty space in the groups pane will bring up the contextual menu
Previously you had to right-click on a group.
Bug fixes:
Dumb quote marks won't be escaped when BibTeX Markup is used for formatting references. Fixed a bug where a right click on empty space in the reference list caused an error warning. Unicode characters in the WiFi sync list are now rendered correctly. Fixed a bug where the BibTeX "don't change case" status wasn't correctly shown when preferences was opened. Fixed several bugs in generating citekeys. Fixed a bug that prevented smart SQL groups with predefined content from being created. Fixed a bug in the format window where changing the Type in one tab didn't update the field names pop-up menu in the other. Fixed problems with the display of scrollbars in the library window right pane. Fixed a bug on library open where the various panes weren't updated to reflect the first selected reference's content. You can once again change the color of text in the edit pane. Fixed a problem where searching for some DOIs failed to find the reference or generated an error. Fixed a bug where the wrong reference was shown in the edit pane. Fixed a bug where the Notes tab could contain light gray hint text. The PDF tag enter field expands if necessary to accommodate pasted text. Fixed a bug where the reference list would become invisible when invoking full screen while the library was in the widescreen view. Fixed a bug where searches for PDF tags could incorrectly match a PDF with a similar name. Fixed a bug where the issue number wasn't imported if it was identical to the volume number. Fixed a reference duplication bug where the new reference was selected but edits were recorded in the original.

New in Bookends 14.0.8 (May 8, 2022)

Changes in importing data from JSTOR. Changes in importing data from JSTOR. JSTOR has made substantial changes that require modifications in how their data are accessed. First, note that if you should log into JSTOR, even into a free account you create, because you may then have access to more references. Second, if you then accept the terms and conditions in your profile, the Accept Terms and Conditions pop-up won't appear each time you download PDFs in a session. Third, access to some references requires IP authentication. Therefore the results are often better if you are using Bookends on your institution's network or via a VPN connection. Bookends will no longer offer to attempt to automatically download JSTOR PDFs. Downloading JSTOR PDFs can still be done, however. If you are using direct JSTOR search, select the reference you want to import and then open Bookends Browser in the bottom pane. Click the Download PDF button (if offered), agree to the Terms and Conditions if necessary, and download the PDF. Import the metadata and PDF using the import pop-up menu at the bottom of the window. If you search with the full screen Bookends Browser and see the down arrow at the top right, click it and import the metadata as usual. Then click the JSTOR Download PDF button in the web page (if offered), agree to the Terms and Conditions if necessary, and download the PDF to Bookends Browser. Once downloaded, either drag and drop the PDF proxy icon onto the Bookends library window, or right-click on the PDF proxy icon and choose among the options. Because of restrictions enforced by JSTOR, Bookends direct search is more likely to be able to download metadata from JSTOR than the Bookends Browser search.
BibTex: improved protection of capitalized words in title. When you are outputting text as BibTeX Markup, Bookends will compare each title word to the list of words whose case is not to be changed (Scan & Bib preferences). If there is a match, and the word begins with a capital letter, Bookends will output it surrounded by curly brackets (e.g. {Paris} or {United States}). This option can be enabled in preferences, BibTeX tab: Bracket "don't change case" words in title.
BibTeX: customize citekeys. In BibTeX preferences tab, you can configure Bookends to create the following citekeys: Author + Year, Author + Year + UniqueID, Author + Year + Partial Title (first 5 meaningful characters), and Author + Year + Library Name. The second and fourth options ensure that the citekey is unique among all of your libraries.
Output linked reference information using a format. To access linked reference information independently of the Inspector, use the % character in a format. Bookends will output the unique id and reference relationship for each linked reference. If there is more than one, they will be separated with semicolons. This could be useful, for example, if you want to obtain linked references using AppleScript. The % character was previously used to output the absolute reference position in the database, which is now obsolete.
Bookends will recognize Markdown URLs in notecards. Select the notecard and right-click, then select the URL from the contextual menu to open it in your browser. If the URL begins with www, https:// will automatically be added.
A right-click now selects the format or import filter in the Formats Manager and Import Filter Manager, respectively. The option to show the import filter in the Finder now only works for items in the Custom Import Filters folder.
Updated right-click behavior in the references, groups, and term lists. A right-click now selects the row and immediately brings up the contextual menu. Previously you had to left-click to change the selection and then right-click to activate the contextual menu.
Bug fixes:
Fixed: an error when scanning with an Author-Date format or when adding Types to a format. Fixed: the formatting function replaced repeated authors with an en-dash or em-dash failed. Fixed: when in dark mode, some PDF tags in the summary view were displayed in black (i.e. invisible). Fixed: the reference selected in the library window could change when switching to another app or the Finder while in the process of creating a new reference. Fixed: selecting nothing from the contextual menu in the groups pane could cause it to resize. Fixed: the same ad hoc attachment folder could be added multiple times. Fixed: eliminated some unnecessary UI updating when syncing references after the library window is deactivated. Fixed: Proofreading Word documents, which was broken in the last update, works again. Fixed: group names changed via AppleScript weren't saved. Fixed: group names changed via AppleScript weren't saved. Fixed: scanning a document containing only citations that were excluded from the bibliography would generate an error.

New in Bookends 14.0.7 (Apr 10, 2022)

Type pop-up menus no longer display Unused Types. When the name of an Unused Type is changed in preferences it will appear in Type pop-up menus. If the name is changed back to name beginning with Unused it will no longer be shown. The exception is that if a reference was assigned a Type that was later changed back to Unused, that Unused Type will be shown when that reference is selected.
The punctuation settings for Cited Pages are now Type-specific. That means that what is output before and/or after cited pages in the final citation can be different for different reference Types.
Show all references in the library window when filtering by Term List. When filtering the library with Term Lists instead of groups, right-click and select "Deselect All Unpinned Terms" to have Bookends show all references. This is useful if you want to add Terms like Keywords to your references by drag and drop on the Term List.
Add Terms to references by dropping them on the Term List. When showing a Term List in the left pane you can drop one or more references on an item in the list and it will be added to all of the references. This is especially useful as a quick way to add keywords. If a reference already contains the keyword, it won't be added again. Note that you must right-click and "Deselect All Unpinned Terms" so that the list shows all references, not just those that already contain the term.
Add keywords to references via a contextual menu. Right-clicking on the keywords field will bring up an Add Keyword option that lists all of the keywords in the library. As with all pop-up menus, typing will take you to the closest corresponding item in the list. Bookends will add the chosen to all of the selected references. If a selected reference already has tha keyword, it will not be added again.
The selection in a PDF will remain when the annotation popover window closes
This means that utilities that cause the popover to close, like PopClip, can be used with Bookends.
Added a keyboard shortcut for Edit -> Copy Hypertext Link -> Copy As Link. Shift-Option-Command-L.
Fields in the edit pane accept dropped text
Enhanced readability of the PubMed automated search results
Type and labels cannot be set to empty in preferences
Bug fixes:
Fixed a rare bug in BibTeX file sync where in certain conditions the contents of the file could be deleted. Fixed a bug where the name of the selected Type above the preferences label list wasn't immediately updated after it was edited. Right-clicking on an edit field when the library has no references no longer shows a hierarchical menu. Fixed a bug where under certain conditions the Type in the popup menu didn't match the data for that Type when the Format Manager was opened. The progress window will now be shown when exporting the selected references using a bibliography format. Fixed a bug that caused edit field hints to be drawn when changing Types even if they were turned off in preferences. Fixed a rare problem where an error message was displayed when the library window was closed.

New in Bookends 14.0.6 (Mar 14, 2022)

Improved JSTOR imports. When using a JSTOR URL to identify the reference to import, Bookends will use the JSTOR APIs to obtain higher quality information. This requires that you have access privileges to JSTOR, and does not work with JSTOR Research Reports (a limitation enforced by JSTOR). A byproduct of this is that Bookends will use the JSTOR.fltr settings to import JSTOR data when it is obtained via the JSTOR URL. If you've modified JSTOR.fltr you should remove it from the Custom Import Filters folder and use the new default filter provided by Bookends.
Improved edit pane display. Changes in label placement and spacing allow more text to be shown in each field.
Showing edit field hint text is optional. A setting in preferences, Refs tab, lets you show or hide hints in edit fields.
Added more escaped BibTeX characters to the Unicode conversion table
Bookends will now import text in cases where the tag and the textual content are separated by a tab
When doing a live search for words surrounded in quote marks, the matching phrase in the Summary view will be highlighted in yellow
Previously each word in the phrase would be highlighted even if they weren't found together.
When importing from bioRxiv in Bookends Browser, Bookends will put 'biorXiv' in the Journal field. Something similar will happen when importing from medRxiv, which had been broken by changes made on their server.
Attach a picture in the clipboard. Use the Refs menu or right-click in the reference list and select Attach -> Picture In Clipboard.
When fetching Google Books cover art, Bookends will change the URL provided by Google to use "https"
Bug fixes:
The Notes tab will once again have an asterisk if the Notes field has content and you are not showing it on the Main edit pane tab. Fixed a cosmetic issue in the edit pane where the hint color would be incorrectly applied to metadata. Fixed a bug where the PDF annotation popover didn't close when it should. Fixed a bug where double clicking on white space in the note stream would cause an error. Fixed a bug where the hyphen-containing citekey in two references weren't identified as duplicates. Fixed a rare problem with importing references Sente. Fixed a bug where downloading the same reference with cover art from Google Books caused a hang. Fixed a bug where the edit field hints reflected those of the last-viewed reference. Fixed a bug in the standalone editing window where hint text could be saved as the content of the empty field. Fixed a bug in the standalone editing window where resizing the window didn't resize the text fields. Fixed a bug where the Action pop-up menu under the group pane didn't fire unless there were user-added groups. Fixed a problem where in some cases there were duplicate entries for the same folder in the ad hoc folder list. Fixed a problem with edit field hints were a & in the label name was output twice. Fixed a bug in the build process where Bookends was incorrectly marked as supporting non-English languages. Fixed a bug in Mellel scans when the first character in a citation is @.

New in Bookends 14.0.5 (Feb 14, 2022)

Share synced libraries with others (requires macOS 11 Big Sur or later). After uploading your library to the cloud, the cloud pop-up menu will have a new option, Share Library. Use it to send an invitation to other Bookends users to allow read/write or read-only access to the library. Once accepted, you (the owner) and others (the participants) can work with the same library. To share attachments, point the library’s attachment subfolder (set in the File menu) to a file sync service folder (e.g. iCloud Drive, Dropbox, Microsoft OneDrive, etc.) that contains the attachments, and use that service’s method to share the folder. If you are sharing with Bookends for iOS, the folder must be in iCloud Drive. Bookends will automate much of this for you when you use the cloud pop-up menu Prepare Shared Attachment Folder.
Specify a library-specific attachment folder outside of the default attachment folder. Use File -> Set Default Attachment Subfolder to bring up a dialog that let's you set an attachment folder for the open library. Click Browse and select the folder you would like to use, and its full pathname will be shown. Note that if you use the pop-up menu instead of the Browse button you will only be offered subfolders in the global default attachment folder. You must use Browse if you want a folder outside of that hierarchy.
Improvements in the edit pane. In Light Mode, the field label text is shown in empty fields as light gray "hint" text. This is not done in Dark Mode, in which the fields are a darker shade that provides guidance. The height of the edit field will adjust as you type if you're autocompleting and the suggested text is too long to fit on one line. Finally, label text size will adapt if you change the size of reference text in preferences. If the reference text size is set to 12 points, the label text size will be 12 points. If the reference text size is 13 points or greater, the label text size will be 13 points.
Improvements in importing authors when a JSTOR PDF is attached
Drag-reorder field labels with a simple click and drag. This previously required that the Command key was pressed.
If Postbox is your email client, sending an email from Bookends will now include attachments. Sending attachments already works with Mail and Microsoft Mail.
Floating citation references will include the volume number of edited books
The annotation popover window will close if you copy the selected text with Command-C or the Edit -> Copy menu
Bookends will search up to the first 5 pages of a PDF for a DOI when it is attached
Bug fixes:
Fixed a bug in the automated search window "find" function. Fixed a bug in preferences where restoring the factory default for the Summary views set incorrect values. Fixed a bug that could result in "record locked" errors. Fixed a crash that occurred if you closed the preferences window with a listbox edit cell active. Fixed a bug where changing some labels would cause an error. Fixed a bug in editing very large fields where deleting text could cause the view to become truncated. Fixed a bug that in rare circumstances could cause the attachments folder to be moved to the Trash. Fixed a bug where the text color would be black after editing a field in Summary view while in Dark Mode. Fixed an issue with saving edited text in Dark Mode.

New in Bookends 14.0.4 (Jan 9, 2022)

All-new reference edit pane. All fields are in a vertical scrolling list. Field sizes automatically adjust to accommodate their content. You can reorder the fields in preferences (Refs tab) or by Command-dragging a field's label and dropping it on the label of another (the dropped field will be moved to the position before the receiving field). You will have to recreate the field order if you had changed it in previous versions of Bookends. If the contents of a field exceed a certain height, a disclosure triangle will allow you to expand or collapse the field. If more than one field has a disclosure triangle, all will expand or collapse together. Cloud Sync will sync the field order between Macs. The All concise view has been removed as it is now redundant.
File -> Export PDF Annotations. This operation export annotations in PDFs attachments. You can choose to work with PDFs attached to the selected references, those in the Hits List, or all references in the library. Annotation contents can be sent to the clipboard or a text file, and you can specify the kind of annotations you want extracted (highlights, underlines, and/or notes), and the metadata associated with the annotations (PDF pathname, the page on which the annotation occurs, and/or the date it was last modified). The page label is extracted from the PDF itself, and may or may not correspond to the page of the published article. Annotations with content (e.g. Notes) usually have modification dates; those without content (e.g. plain highlights) usually do not.
Right-click on the PMID or PMCID fields and obtain a contextual menu that will open the article in your browser. This already exists for the URL and DOI fields.
If you try to sync a BibTeX file but none of your references have citekeys a message will explain why nothing was saved
In the edit pane, clicking on the color label name at the top will bring up the pop-up menu allowing you to change colors
Improvements in importing metadata from JSOR when attaching a PDF. Note that the data can be incomplete because JSTOR is inconsistent in providing it. The direct JSTOR search imports higher quality information.
Bug fixes:
Fixed a bug that caused Bookends to mistakenly create the folders /Bookends/Attachments when the default folder was set to iCloud in preferences. Fixed a bug where a right-click on an underline notecard offered the possibility of editing it. Fixed a bug in BibTeX sync where extra @ characters were added at the beginning of the first reference. JSTOR PDFs will no longer be attached to the wrong reference if there is an error when trying to import the metadata. Fixed a bug where Global Change -> Move Attachments of the selected references didn't work. Fixed a bug where an error was thrown when moving attachments to a top level folder. Fixed a crash in the Online Search window when a search hadn't been performed and the Find -> Done button was clicked.

New in Bookends 14.0.3 (Dec 12, 2021)

Manipulate PDF annotations with a contextual menu. Right-click on an annotation type that Bookends supports and you’ll see a contextual menu that lets you delete, copy, edit contents, or change the color, depending on the type of annotation selected.
Turn on continuous highlighting and set the selected text to the desired color by pressing Control-1 to 5 when the annotation popover window is active
Global Change -> Move Attachments. This function lets you move or copy the attachments in your selected references, the Hits List, or in the entire library to a folder of your choice. There is also the option to remove annotations from PDF attachments as they are moved or copied. This would be useful if, for example, you created a library-specific attachment folder and wanted to move all the attachments in that library to the new folder.
Watch folder improvements. Bookends will create only one reference when downloading very large files from a browser to the watch folder..
The author/editor separator field is disabled in the BibTeX import filter. BibTeX expects names to be separated with " and ".
Created a keyboard shortcut for Copy DOI (Shift-Command-G) and added this option to the reference list right-click contextual menu
The default attachment folder pop-up menu in preferences now offers “Bookends iCloud Folder” as an option. This was previously “iCloud Folder For iOS Sync”, but was changed to reflect the fact that because Bookends 14 uses native cloudKit, it can create this special dedicated folder itself.
When present, subtitles will be added to the title of books found on Google Books
Bug fixes:
Fixed a bug that could corrupt the preference file containing the reference Types and labels. Add an extra check to prevent an ad hoc attachment folder from being added more than once. Fixed a bug where libraries weren't being synced on open. Fixed a bug where the PDF comment size setting in preferences wasn’t saved. Fixed a bug in the Formats Manager where the controls for setting case options could be invisible if the window was resized. Fixed a with custom formats where the bibliography example in the format window would be empty if the citation example was empty. Fixed a bug with the BibTeX sync file where the leading @ of an edited reference was stripped off. Fixed a bug where the wrong crosslink type was added to a reference when the link preference default was changed from Book:Book Section. Fixed a bug where resetting the concise views to the factory defaults in preferences wasn't saved. Fixed a problem where syncing preferences could result in a "503" error. Fixed a bug in the automated PubMed search window where the entire metadata field could have a background yellow color.

New in Bookends 14.0.2 (Nov 7, 2021)

New PDF annotation popover. When you select text in a PDF, a small floating window allows you to set the highlight color (or none) and offers the following choices: Highlight, Underline, Copy, PDF Note, Notecard, Quote. Clicking Highlight, or double-clicking a highlight color, will highlight the selection (if no color is selected, the window will simply close). PDF Note will create a new PDF note that contains the selected text. Notecard will make a new notecard containing the page number and the selected text as the body, and Quote will make a new notecard with the page number and use the selected text as a quote. If the PDF is displayed in the PDF view pane, Notecard and Quote will open the note stream and display the new notecard. If the PDF is displayed in the edit pane Attachments tab, the selection will be added but the edit pane will remain. The floating window is dismissed when you click a button or click outside of the window. The items in the old Action pop-up menu that performed these functions have been removed.
Improved UI for setting PDF highlight colors. You can change the color, or restore the default color, of the 5 PDF highlight options with a right-click. Click on the chevron next to the marker icon in the PDF toolbar and then right-click on the color you want to change. The contextual menu will let you select a new color (Change Color) or restore the original (Restore Default Color). Previously, these actions were performed with difficult-to-remember key-click combinations.
Added a keyboard shortcut for Make Note in the PDF viewer: Shift-Command-E
Automatic retrieval of PDFs from PubMed Central. If Bookends is unable to fetch a PDF from the publisher for an article imported from PubMed (e.g., if you don’t have journal access privileges), it will check to see if it's available from PubMed Central and, if so, download it from there.
Certain types of errors in a format will be automatically repaired when it is opened in the Formats Manager
A sync warning will be issued if your library is stored in iCloud Drive even if it is not in the Bookends iOS sync folder. Sync will be suspended for the current session, and can be re-enabled after you move the library file in the Finder.
Updated Bookends Browser to maintain compatibility with certain sites
The $ sign won't be escaped with formatting using BibTeX Markup
Updated database engine
Editing PDF file tags works in Monterey
Bug fixes:
Fixed a rare bug where using a legitimate format could result in an error. Fixed a problem where EndNote PDFs weren't being transferred when importing from EndNote. Fixed a bug where the tag was still added after canceling the addition of a PDF tags to multiple selected references. Fixed a bug in the concise views where the name of file tags could be colored incorrectly. Fixed a rare problem where the first reference list column could be hidden.

New in Bookends 14.0.1 (Oct 11, 2021)

Create peer-to-peer reference links directly in the library window:
When two or more references are selected, the menu option “Link Selections (Peers)” will be enabled in the Refs menu and the right-click contextual menu. This option will create peer-to-peer links even when the Links Inspector is not open. Note that if the references already have a link relationship, it will be changed to peer-to-peer.
Create a synced .bib file containing all your references in BibTeX format:
This is a one-way (Bookends -> file) sync on demand, which may be useful to those who use Bookends references with other apps such as LaTeX, Pandoc, or TeXstudio. To initiate, use File -> Create Synced BibTeX File. Once created, the menu will read Sync Linked BibTeX File. When this is invoked, Bookends will update the file with references added, deleted, or edited. Note that Bookends stores the .bib file's alias, so you may rename it or move it to another location on the HD and Bookends will still find it. If the file has been deleted or is stored on an external drive that is not mounted, the menu will revert to Create Synced BibTeX File. Bookends identifies references by their citekey, so any references without citekeys will not be synced to the linked BibTeX file. This function uses the format "BibTeX.fmt". If you have created an alternative BibTeX format with a different name, you must rename it to BibTeX.fmt to be used for syncing. Note that this function has nothing to do with cloud sync -- it just maintains a local .bib file that can be synced (updated) on demand to match your library.
BibTeX format updated:
Fields with missing content will no longer be output, which in many cases will improve processing speed and reduce the size of export files.
The names of saved advanced PubMed searches can be of any length:
Previously they were limited to 31 characters.
If an error occurs during sync, Bookends will offer to "Force Full Sync", which will often override the problem and allow the sync to finish:
You will also have the option to temporarily suspend syncing during the current session.
When an item from a term list for a non-scrolling field (e.g. Journal) is dropped on a reference, the contents of the corresponding field will be replaced:
Previously, the item was appended to the existing text.
Bug fixes:
Fixed a bug that prevented AppleScripts from working. Fixed a bug in floating citations where pressing Return or Enter didn't insert the temp citation of the selected reference. Fixed a bug in the inspector's Rename Attachment function. Fixed an error that would occur when clicking on the inspector’s import icon when there were no references in the list. Fixed a bug where duplicating a reference could cause and error on sync. Fixed a rare problem where the online search list of references could become unresponsive. Eliminated an unnecessary dialog in the inspector asking permission to detach a PDF that was moved to the Trash. The characters " and # will be excluded from citekeys generated by Bookends.

New in Bookends 14.0.0 (Sep 12, 2021)

Bookend 14 has a new bundle id: This means that older versions of some apps that integrate with Bookends (e.g., Mellel, Nisus Writer Pro, DEVONthink, and Tinderbox) will not be able to send AppleEvents to Bookends 14. We have worked with each of these companies and they have or will release updates that work with Bookends 14.
Introducing cloud sync version 2 (v2): The original Bookends cloud sync (version 1) used Apple's CloudKit JS APIs, which give web apps access to iCloud. Bookends now uses Apple's native CloudKit. You must be signed into iCloud and have enabled iCloud Drive in System Preferences to sync. The major advantage at this time is that v2 uses your macOS iCloud account information, meaning that there is no need to log in separately to iCloud in Bookends. Importantly, native CloudKit will allow us to expand Bookends' sync capabilities in future releases.
Much improved PDF search results: The results of a PDF search will be listed, with the bolded search word shown in context along with page where it was found. Clicking on an item in the list will take you to its location in the PDF.
New Cited By Inspector: If the parent reference has a PMID this inspector will use PubMed to find all of the references in which it has been cited. You can view a reference in your browser by double clicking on it, or import it by clicking the download button, right-clicking, or drag and drop. When using the first two methods, you have the option to automatically link the imported reference to its parent. Note that the references found by PubMed may or may not correspond to other sources that track citing references. Hover the pointer over a reference to see the full contents in the help tag.
Cited In Inspector adds PubMed as a source: If the parent reference has a PMID Bookends will use PubMed to find which references are cited in the parent reference. PubMed has much more information about cited references than CrossRef and the results are resolved much more quickly. If there is no PMID and the parent reference has a DOI, Bookends will use Crossref as before. From the inspector you can view a reference in your browser by double clicking on it, or import it by clicking the download button, right-clicking, or drag and drop. When using the first two methods, you have the option to automatically link (work: work cited) the imported reference and its parent. Hover the pointer over a reference to see the full contents in the help tag.
The two Cited Inspectors won't change the parent when used to import references
The way that Link Inspector relationships are created and synced has been completely rewritten. Although transparent to users, this will make it easier to add improvements in the future.
The Attachments Inspector now shows each attachment’s path name
Added a peer-to-peer relationship to reference links: This is useful if you want to link references that do not have a hierarchical relationship, for example references cited in a paper (article-to-article) or chapters in a book (chapter-to-chapter).
Various modifications to the Link Inspector: The ability to add comments to individual linkages has been removed. Cosmetic improvements.
Double clicking on a reference will not toggle the edit pane or PDF viewer if the Links, Cited In, or Cited By Inspector is open. In those cases it will simply set the Inspector parent to the reference clicked on. Previously, it would do both.
Show attachment names in the reference list column view: You can set this in preferences (Lists tab) or with a right-click contextual menu in the reference list. Names of multiple attachments belonging to the same reference will be separated with semicolons.
Use Bookends Browser to replace an orphaned attachment: Select the reference with the orphaned attachment and open Bookends Browser in the display pane. Depending on the URL stored with that reference, the browser will display either the PDF or the reference's web site from which you can navigate to the PDF. Click the paper clip attach icon and the PDF will be downloaded and replace the existing orphaned attachment. Note that if you have more than one attachment, orphaned or not, Bookends will simply add the PDF to the attachment list and you should detach the orphaned attachment yourself.
The reference list contextual menu "Sort By Label" has been changed to "Group By Color". This reflects the difference between sorting the Label column, which is ordered by the text assigned to each color, and this function, which groups references with the same color.
Bibliographies sent to disk as UTF-8 or UTF-16 will have the extension .txt. If output as Plain Text, the extension will be set to .ris if the RIS format is used.
There is a new AppleScript property to get the path to a library's default attachment subfolder, if any (library attachments subfolder path). If no library subfolder has been set, Bookends will return the path to the default attachment folder itself.
Typographic quote marks will be converted to their BibTeX equivalents when "BibTeX Markup" is specified for the formatted output
A reference’s unique ID can no longer be changed by the user: Too many features that depend on the unique ID and would break if it were changed.
On launch Bookends will check for and "forget" ad hoc attachment folders that are in the Trash
The reference list right-click contextual menus have been modified. Right-clicking on the paper clip icon now only shows options relevant for attachments.
Improved user control when downloading PDFs: A Skip button in the PDF -> Download From Internet dialog immediately stops the attempt to get the current PDF and moves to the next selected reference, if there is one. This is useful if the online source is slow to respond or hangs, and is more reliable than pressing Command-.
Online searches can be stopped by clicking the progress wheel. This is more reliable than pressing Command-.
Improved Autocomplete Paper UI: The sheet remembers its dimensions between openings during a session. When references are found, the default button changes from Search to Import, and import will be triggered by pressing the Return key.
When fetching metadata using PDFs downloaded from pre-print servers like bioRxiv and medRxiv, Bookends places the name of the pre-print server in the Journal field
Note that once the paper is published that version will receive a new DOI.
Any text in the live search field will be selected after you select and group and the reference list is updated. This makes it easier to delete if you no longer want to filter the results.
If present, the following characters will be removed from automatically-generated BibTeX keys: ’&^
When attaching a PDF whose reference already exists in the library, you will still have the option to attach to a new reference and import the metadata. This is be useful if, for example, you are adding separate PDFs for a book and its chapters.
Bug fixes:
Fixed the format of the date in the Added column when duplicating a reference. Cosmetic fix for the display of the selected reference’s text in the Link Inspector when it is in the background. Fixed a crash that could occur in Big Sur when running the Bookends demo on the same machine where there was an old version from the Mac App Store. Fixed a bug where failure to close the color picker in preferences could lead to an error message. The Google Books online search now responds to Command-. Fixed a bug that prevented changes to Types and field labels from being synced via the cloud. Fixed a bug where styled text in the Short Title field wasn't toggled to plain when it should be when formatting. Fixed a bug where the Attachments Inspector and pop-up menu of attachments weren't updated immediately after reattaching a file. The Attachment dialog subfolder pop-up menu will no longer show folder aliases the user placed in the default folder. Fixed a bug where the links column didn't update immediately when replicating a book as a book chapter. Fixed a bug where starting the watch folder without it first would result in the import of hundreds of files from the Bookends bundle. Fixed several bugs in the marooned file inspector that could cause a file to be listed as marooned even if it wasn't. Fixed a bug in several printing functions that resulted in white text on a white background when in Dark Mode. Fixed a bug in Pages scanning where the format's hanging indent setting was only honored for numbered bibliographies. Fixed two bugs in creating a bibliography in Dark Mode where the output was either black text on a black background or the file sent to disk was empty. A leading > for a comment will be excluded when copying the contents of a notecard. Fixed an error that could occur when the library was synced as it was closed. The color for a color label is now positioned correctly in the Summary view. Fixed an error that could occur when clicking on certain types of PDF annotations. Fixed a bug that in rare instances would cause an “illegal cast” error. Fixed a bug where user-defined Term List weren't remembered between launches. Fixed a bug in the PDF search field when a recent menu item was selected. Fixed a bug that prevented autofilling of individual fields from working. Fixed a bug that could cause a PDF to be scrolled to the end when opened by changing references using the arrow keys. Fixed a bug that caused the text of a field edited in the enlarged field window and then saved in Dark Mode to be 2 points too large and black. Fixed an error that could occur when dragging a reference from the floating citation window to a Mellel document.

New in Bookends 13.5.5 (Jun 7, 2021)

Restored direct downloading of PDFs from publishers that use ScienceDirect
This requires access privileges.
Drag files from the marooned attachment list:
Dragging the selected files is like dragging the files in the Finder. You can move them to another folder, drag them into an “Open File” dialog, drop them on a Bookends library window to attach them, etc. If the files are moved the list will automatically update.
Right-click to refresh the list of files in the marooned attachment list:
This may be useful if, for example, you’ve opened another library that has attachments and want to regenerate the list without having to close and reopen it.
Attaching multiple files to the selected reference has been streamlined:
When you drop more than one file on the library window, one of the options in the resulting dialog is "Attach To Selected Ref". If you select this option a second dialog will offer to rename the files and/or move or copy them to the default attachment folder. These options will be applied to all the files in the drag without further user intervention. In previous versions this dialog would appear for every file in the drag.
Create a notecard with a title from a PDF's table of contents:
When the PDF's table of contents is showing, right-click on an entry to add it to the note stream as the title of a new notecard. If the note stream is showing the notecard will be opened for editing, so you can add content if you want.
When formatting as BibTeX Markup, institutional names (i.e. those terminated with a comma) will be surrounded by curly brackets
Bookends will identify damaged PDF attachments and offer to show them to you in the Finder
Previously, trying to display a damaged PDF would result in a cryptic error message which could be mistaken for a crash.
When searching a PDF, pressing Shift-Command-G will find the previous match
As before, Command-G fill finds the next match.
medRxiv was added to the Bookends Browser bookmarks
This will be seen in new installations of Bookends.
The last run date for a saved search won't be updated if an error occurs
Group names in the manual remove duplicates window are read-only, and an explanatory dialog will appear if you try to do edit them
Preferences changes to library window fonts/sizes are updated immediately
You can show URLs created with OpenURL in the library window browser (default), Bookends Browser, or your preferred macOS standalone browser
These options are available in the Metadata tab in preferences.
The Action pop-up menu below the reference list has been removed
These functions and more are provided by a right-click hierarchical menu.
Bug fixes:
Fixed a bug in exporting references to a tab-delimited file. Fixed a bug where a space was used instead of an underline in front of the disambiguating number when renaming attachments. Pressing the cancel button when attaching multiple files at once cancels the entire process, not just the attachment of that one file. Fixed a bug that prevented the progress window from showing when exporting selected references with a format. Fixed a bug that caused Bookends to add a non-PDF attachment to the selected reference even if you indicated it should be added to a new reference. Fixed a bug where selecting “Open” from the hierarchical menu would not open graphic attachments such as jpgs. Fixed a problem that could cause an error in some situations if the color picker wasn't manually closed. Fixed a bug in manual verification of remove duplicates where a modified attachments field wasn't updated in the database. Fixed a cosmetic problem when switching from a boolean search to Bookends Browser in the Online Search window.

New in Bookends 13.5.4 (May 3, 2021)

File -> Export References provides more flexibility and a cleaner user interface: You can now use a hierarchical menu to export the selected references or the Hits, decreasing the number of dialog windows that need to be dealt with. Previously you could only export the Hits. These options have also been added to the reference list right-click contextual menu.
Improved marooned attachment manager: Right-click on the list to move the selected files to a folder or the Trash. Press Delete to move the selected files to the Trash. Moving many files at once is much faster.
Bookends will select the default reference Type, set in preferences, when populating the Type pop-up menus in the Format Manager: Previously it selected Journal Article regardless of the user’s preference setting.
New color picker: The color picker has been modernized and is now asynchronous. That means that changes in a color are immediately reflected in the associated control. In addition, the new color picker fixes a problem some Big Sur users experienced where selecting a color resulted in sluggish behavior.
Swap columns in the reference list by right-clicking in the column and choosing the column to swap with
The full URL will be displayed in the concise views (Summary and All), not a truncated version
Added "More than one attachment" to the pre-defined Smart (SQL) groups
You will receive a warning if the default attachment folder is unavailable (e.g. on an unmounted server) and has been reset to the factory default
Clickable email links work in Bookends Browser
Use swipe gestures to change pages in Bookends Browser: Swipe between pages with one finger can be enabled in System Preferences -> Mouse -> More Gestures.
Improved trapping of illegal characters entered in the Autocomplete Paper text fields
Updated database engine
Bug fixes:
Fixed a bug where Bookends would misidentify a file as marooned if it contained certain characters, such as parentheses or question marks. Fixed a bug where file bundles (e.g. TextEdit RTFD files) were treated as folders and their internal contents identified as marooned attachments. Fixed a bug that could cause a hang when performing an Autocomplete Paper using Google Books. Fixed a bug that prevented the PDF annotation color icon from changing appearance immediately after the color was edited. Fixed a bug in Wi-Fi sync of attachments. The lack of an annotation modification date will no longer cause an error when filling out the note stream.

New in Bookends 13.5.3 (Apr 5, 2021)

Marooned Attachments Manager: A marooned attachment is a file in an attachments folder that is not attached to any references. File -> Show Marooned Attachments generates a list of files that aren't attached in any open library. It is important to note that Bookends can only check open libraries for the presence of an attached file -- if you have unopened libraries the "marooned" file may actually be attached in one of those. It's up to you to make sure all your libraries are open when you invoke this function. Once identified, you can press the space bar to open a file in Quick Look, double click to open it in your PDF reader, or show it in the Finder. A pop-up menu lets you move the selected files to a specified folder or the Trash. Some users may have attachments on the Desktop, making the Desktop an ad hoc attachment folder. Because the Desktop will undoubtably have files unrelated to Bookends, by default Desktop files aren't listed. However, there is an option to show potentially marooned Desktop files if you want to see them.
When attaching to a PDF to new reference with Autocomplete Paper, Bookends will import the PDF's title and subject if they are found in its metadata. If Autocomplete Paper is successful these will be replaced by the information imported from the online source.
Images (non-PDFs) in the display pane can be moved to the Finder or another app by drag and drop. A copy of the original will be delivered to the dropped location. To create an alias of the image, hold down the Option and Command keys and then drag.
When an image is showing in the display pane, the right-click hierarchical menu has options to open the image, zoom the image, and show the image file in the Finder. Opening the image with a double click has been removed because it conflicts with drag and drop.
The jpg files of cover art imported from Google Books will be named using the same rules as when renaming attachments. Previously, they were named "Download" followed by a random number.
Bookends Browser detects DOIs for articles from The Lancet journals and does a better job downloading their PDFs
When searching PubMed in Bookends Browser, Bookends will find a PDF's metadata even if it hasn't been assigned a DOI
Set the font and font size for PDF comments in Preferences
References of Type Review will be treated as Journal Articles when formatting an entry in the Vol (Issue) field. That is, the volume and issue can be output together or independently.
Live Search will perform a string (character) search for characters enclosed in quote marks. Previously this search would only match whole words.
Added PDF Viewer as an option for viewing in PDFs in another application
Bookends Browser will now allow you to download PDFs from OVID via the PDF proxy icon or the paper clip
If an article found on PubMed with a direct search lacks page numbers but has an electronic location, the latter will be inserted in the Pages field on import
Updated the PubMed parser to import the correct DOI when the data provided by PubMed contain multiple DOIs of cited references
Bug fixes:
Fixed a bug in which a name with an apostrophe caused an error when generating a BibTeX key. Fixed a bug in "Make PDF note from selection". Fixed an error that could occur when attaching hundreds of PDFs at once. Fixed a bug in cloud sync that caused an error when linking to an existing library in the cloud. Fixed a bug that caused an error when attaching a PDF whose contents could not be read. Fixed an error that occurred when doing a find again in a PDF with after changing the selection. Fixed a bug where the secondary order field in a format wasn't used unless the scan generated a bibliography. Fixed a bug that could cause an image in the display pane to persist when a search found no matching references. Fixed an error that could occur when switching references with an attachment being shown. Fixed a bug when deleting references from very large libraries. Fixed several problems with Wi-Fi syncing of attachments. Fixed a problem where using the Temporary folder as an ad hoc attachment folder generated errors in Catalina and later.

New in Bookends 13.5.2 (Mar 7, 2021)

Major code refactoring of many core functions: The code has been modernized and streamlined.
The icons in the PDF thumbnail view are larger, making it easier to distinguish the contents of one page from another
Subject Bibliographies now display super/subscripts when sent to the Bibliography Window
When Bookends is watching the Downloads folder for PDFs, files ending in ".pdf.part" will be ignored: These files represent partial downloads in progress and should not be attached until they are complete.
Spotlight queries now search ad hoc attachments folders as well as the default folder/subfolders
You are able to use default attachment folder subfolders to any depth when attaching files: This was previously limited to just root level subfolders.
When searching PubMed in Bookends Browser, Bookends will find a PDF's metadata even if it hasn't been assigned a DOI
Added a keyboard shortcut for New Static Group: Option-Command-G
Added PubMed Central to the Bookends Browser default bookmarks: This will appear only for new installs. If you are upgrading, have not previously edited the bookmarks, and want this entry in your bookmarks, remove the Bookmarks file from the Bookends folder. The new default settings will appear after the next launch.
The modification dates shown for annotations in the note stream now include seconds
Changed the Term List keyboard shortcut to Option-Command-; to avoid a conflict with the Check Spelling Now menu
Attaching a file in the Trash is no longer allowed
Updated database engine
Bug fixes:
Fixed a bug where moving to another reference using the Links Inspector could cause edits to a reference field to be discarded. Fixed a bug where creating a new format based only on the first Type of the selected format would result in an error. Fixed a bug that prevented Bookends QuickLook from working. Fixed bugs in scanning with formats that have a secondary order field for citations. Refs -> Generate BibTeX Key works again. Fixed a problem in Bookends Browser where trying to download a .docx file would cause Bookends to hang. Fixed a bug that could prevent a PDF from being moved to the trash via a menu option if a file with the same name was already there. Fixed a bug that was introduced in 13.5 where importing from Zotero failed to import attachment file names. Fixed a bug in the column view where the first time it was used the indicated sort order was incorrect. Fixed a problem where an error could be generated when closing the online search window in the middle of a search. Fixed a bug in the watch folder where the same PDF could be added to the library multiple times when files were copied rather than moved. Fixed a bug in scanning .odt files where the presence of hard returns (line breaks) would result in an error. Fixed a bug that caused operations that opened PDFs in the default viewer to fail. Fixed a bug in Spotlight Search where Bookends ignored attachments whose names contained a slash. Fixed a problem with scanning some Mellel documents on M1 Macs. Fixed a bug that prevented bibliographies from being placed in the clipboard after scanning RTF files. Fixed a bug that allowed the addition of the default attachment folder and subfolders to the ad hoc attachment folder list. Fixed a bug that prevented hypertext links in notecards from showing with right-click. Fixed a bug in notecard word wrap.

New in Bookends 13.5.1 (Feb 10, 2021)

New in Bookends 13.5.0 (Jan 18, 2021)

New in Bookends 13.4.8 (Dec 7, 2020)

New in Bookends 13.4.7 (Nov 9, 2020)

Restored importing from JSTOR - Importing references that weren't available via free access had been broken because of changes made by JSTOR.
Requests to Crossref are faster and more reliably return a DOI
The PDF command "Make Notecard from Selection and Page #" places the quoted text on a new line
Bookends will offer to unlock a PDF that is locked in the Finder when you try to add or edit a PDF tag, or click on the lock icon in the PDF toolbar
Updated automated download of PDFs from ScienceDirect to deal with changes made by the publisher
Improvements in scanning LibreOffice .odt files
Improved handling of cases where you try to register Bookends on a new Mac with a registration code whose 2 years of free updates has expired
Author names terminated with a comma will be output as entered for Author-Date citations
In the Attach dialog the pop-up list of subfolders to which the file could be moved is sorted alphabetically. This fixes a problem introduced by the APSF file system. Only top level subfolders will be shown.
Close the Quick Look PDF display with Command-W without closing the library window
Bug fixes:
Restored detection of drag and drop of PDFs and other files types onto the Bookends icon in the Dock. Fixed a bug in Live Search that allowed Spotlight searches to be initiated with every keypress instead of when a Return is pressed. The contents of the edit pane attachment tab will be emptied when no reference is selected. Fixed a bug that prevented Live Search of notecards from finding tags (i.e. when the tag word is preceded by %). Fixed a bug where PDFs with slashes in their names weren't displayed in the edit pane Attachments tab. Fixed an error that could occur when searching Google Books. Fixed a bibliography bug were references could be output in small caps if the default bibliography and reference font sizes were 3 points apart. Fixed a bug in secondary citations where "et al." was output after the surname even if Surname Only was selected. Fixed a bug where any groups selected in the groups pane were deselected when a PDF was dropped on it.

New in Bookends 13.4.6 (Oct 5, 2020)

New in Bookends 13.4.5 (Sep 7, 2020)

Elect Hits Group is a new menu item in the Hits menu
The keyboard shortcut is Shift-Command-H.
When searching a PDF, all matches will be highlighted as they are in Preview
Note that in some cases the highlight will be blue, not yellow, until you scroll to another page and back. This is a cosmetic bug in macOS.
Command-Option drag of the PDF proxy icon in the PDF toolbar will create an alias of the PDF when dropped
This is in addition to the normal behavior where dragging without keyboard modifiers will create a copy of the PDF when dropped.
When searching PubMed, the lower pane in the Online Search window will show the article on the publisher's web site if it can
If not (entries in PubMed may lack that link), Bookends will default to the article on the PubMed web site.
Improvements in the PDF toolbar when the width is too narrow to display all controls
Bookends can insert a space in front of a semicolon separating multiple citations in a group
This option is in the format's Citation Options- > Common Settings section.
If Bookends can't search the PDF for a unique identifier when attaching because it is corrupted or perhaps just an image, the alert dialog will include the name of the PDF
Autofill will accept JSTOR URLs that use jstor.com in addition to those using the standard jstor.org
Improvements in Wi-Fi sync
Attachment Inspector improvements
You can resize the list showing attached files. The contents of an attached folder are sorted alphabetically (this is now true in the attachment display pane pop-up menu as well). Reordering attachments by drag and drop is disabled when a folder is attached (the list is always sorted).
When editing a PDF note in Dark Mode the background color will be made black (instead of yellow) to make reading the white text easier
When updating PubMed references with Autofill From Internet, Bookends will remove HTML tags for italicized text from titles
Added a confirm dialog before performing a Global Change Move or Change
Improved the detection and correction of invalid DOI candidates when using Bookends Browser
Bug fixes:
Fixed a bug that caused the PDF page number and the highlighted text to run together when adding a highlight to the Notes field. Unlike highlights, clicking on a note card showing a PDF underlined text annotation will not permit its import into the library. Fixed a bug where the Add Note pop-up menu under the note stream was enabled when no reference was selected. Fixed a bug that caused some fields in the edit pane to incompletely refresh their contents when moving between references. Adding cited pages to a BibTeX citation in the Copy Citation With Modifiers dialog now works. Fixed a bug where tag cloud stop words were applied to file tags. Fixed a bug where a Finder tag might not be refreshed when switching between PDFs. Fixed a bug in Compare References where the field from the wrong reference might be moved when Command-clicking on the field symbol. Fixed a bug in scanning a text file with BibTeX citations where a citation wasn't found if it was preceded by a modifying metacharacter (e.g. ^, %, etc.). Fixed a bug that prevented a right-click on a display pane image of a file in an attached folder from bringing up the hierarchical menu that allows zooming. Bookends will add the extension .bdb to any Bookends 9 library that is converted to the current database schema. Fixed a problem that could cause Bookends to incorrectly identify the default email client. Fixed a bug in Global Change where an error occurring when moving date from a styled text field to one without styles. Fixed an issue in Bookends Browser where you might be prompted to save login credentials when no login as done.

New in Bookends 13.4.4 (Aug 3, 2020)

Widescreen layout - A menu option in the View menu lets you toggle between the compact view, where the display pane for PDFs, formatted references, etc. is shown beneath the reference list, and the new widescreen view, where the display pane is shown between the reference list and the right info pane. You may prefer the widescreen view when, for example, reading PDFs with the note stream open. Unlike the compact view, when in Full Screen all library window panes will be available while you work.
New Speech toolbar icon - This icon is not in he default control set, to use it you must right-click on the toolbar and customize it. Place the cursor in a text field and click the Speech button. Bookends will read the field's contents, or just the selected text, if any. Click on the Speech button again to stop Bookends from speaking.
Double click a reference to toggle the edit or attachment pane open or closed - Which pane a double click opens is set in preferences. Previously, a double click would only open the selected pane.
The text size for the Summary view will be the same as for the Note Stream - Both are set in Preferences with the Note Stream & Summary pop-up menu.
When using unique id in a reference to create a hypertext link in a concise view, Bookends will ensure that what follows the # is a number before creating the link
Renaming an attachment via a right-click on the reference list will allow you to edit the proposed name if there is only one reference selected and it has only one attachment
Added bioRxiv to the Bookends Browser default bookmarks list - This will only be available when performing a new install.
Updated Quick Add to accept URLs from jstor.com as well as jstor.org
Bug fixes:
Fixed an error that occurred when switching a reference list column header to Date Added. Fixed a bug that caused Bookends to hang if the Delete button was removed from the library window toolbar. Fixed a bug where the bibliography was output with white text when scanning a Word document in Dark Mode and using a numbered format. Fixed a bug in scanning a NWP document when in Dark Mode where NWP would treat the bibliography as simply text and couldn't unscan it. Fixed a cosmetic issue where in specific cases the selected reference could be displayed as white text when the list lost the focus. Fixed a problem when importing multiple PDF in batch where matching references already exist. Fixed a permissions problem in Catalina where a PDF annotated in iOS wasn't downloaded by wi-fi sync.Fixed a rare problem where when opening a non-PDF in a third-party app Bookends would try to use the default PDF reader.

New in Bookends 13.4.3 (Jul 3, 2020)

Updated the JSTOR parser to deal with changes made by JSTOR
Improved error handling when a PDF download times out
Updated the COinS parser for WorldCat
Updated the COinS parser for WorldCat
Enabling the PDF continuous highlight marker will highlight any text already selected
PDFpenPro was added to the list of external PDF readers that Bookends will offer as an option to open a PDF
Database engine updated
Improved Bookends Browser:
Bookends can display web pages and PDFs with atypical URIs, has more safeguards to prevent Google Scholar from thinking you're a robot, and can resolve Google Scholar reCAPTCHAs if you are challenged to prove you're a human.
Import PDF attachment names with import filters:
Import filters now accept tags that tell Bookends to put the contents of the field into the internal attachment field. This is useful if you are exporting from another reference manager with a tagged format like RIS and want the attachments transferred to Bookends (previously this was only possible when exporting/importing EndNote XML). Note that you should import only the file name, not its path. If you import a path Bookends won't find it. After import, move the actual attachment files to the Bookends default attachment folder so they can be found.
Insert attachment names from any field into the Attachment field with Global Change -> Move Field:
This is for power users and may be useful if you imported attachments names from another source into a normal Bookends field. This feature will allow Bookends to recognize them as attachments, and if the file of that name is in the default attachment folder Bookends will display it.
New preference option to allow/disallow Bookends from forcing downloading of attachments in iCloud Drive that were moved to iCloud
This option is in the iOS tab and the default is "allow".
When responding to a hypertext link from another app, Bookends will initially search the current list of references:
If not found, all references will be displayed and the matching reference selected. This will prevent you from being taken out of a group if it isn't necessary.
The group All will be selected if you import references with a non-static group selected:
This ensures that the imported references will be highlighted. If a static group is selected, they will be added to that group.
Different Title Case settings can be specified for the titles of a book chapter and the book it is in:
This option appears when you select the Book Chapter Type in the Formats Manager.
Bug fixes:
Fixed a bug where the top of the reference list could obscure the PDF toolbar in full screen view.
Fixed two bug where the text in bibliographies generated for Nisus Write Pro or saved directly to disk as RTF was in Dark Mode was white.
Fixed an issue with some imports from JSTOR where titles were truncated if they contained a quote mark.
Improved trapping (ignoring) of invalid entries in the Quick Add dialog.
Bookends will now work if you mistakenly remove the live search field from the toolbar.
Fixed a bug in cloud sync that could prevent the library from being opened with a "record locked" error message.
Fixed a bug in the reference list view where the sort after pressing the header was not in the correct direction.
Fixed a bug in editing or copying of notecards where some characters, including smart quote marks and apostrophes, were lost.
Fixed an error that occurred when using the keyboard shortcut to go to the PDF find box.
Fixed a problem where having the location of cited pages specified in the citation options tab would result in the removal of any text styles if cited pages weren't included in a temp citation.
Fixed a problem where some Unicode characters didn't appear in the formatted reference.
Fixed a bug when using a menu to move groups to a nested folder where the UI would initially show the groups in the wrong folder.
Fixed a bug in wi-fi sync where an error sometimes occurred when syncing a new Mac library with one that existed on the iOS device.

New in Bookends 13.4.2 (Jun 5, 2020)

Automated group repair - Bookends will determine the integrity of the group hierarchy when a library is opened. If irregularities are found they will be repaired. A repaired group may be moved out of a folder and placed at the root level if its intended location couldn't be determined.
Bookends will force PDFs in the iCloud Drive folder to appear on the hard drive if you have Optimize Mac Storage turned on. This is necessary because Bookends can't find PDFs that were removed by macOS and stored only in the cloud.
Underlined PDF text will be shown as underlined in the corresponding notecard
Improved visuals in Dark Mode
The text color in reference list rows with color labels is dynamically adjusted to be more readable
Text dragged and dropped into a reference field will be appended to the end of any existing content
Perform recent and smart SQL group searches from the SQL search window. An action pop-up menu will display saved smart SQL group searches and any recent ad hoc searches you have done, which when selected will be performed instantly. The list of recent searches is temporary and is reset between launches. If you want to use these searches between sessions, make create a smart SQL group.
If you are running Catalina and you encounter an error when converting an old library, Bookends will offer to open System Preferences -> Privacy so you can give Bookends Full Disk Access permission
Updated the way Bookends Browser finds PDFs when importing from Google Scholar to deal with changes made by Google
When a reference is changed or refreshed, the browser view in the bottom pane will not reload if the URL in the URL field is the same as the one for the reference. PubMed users note that the stored URLs that worked with the old PubMed site are no longer valid. You can correct that with Global Change -> Find And Replace, searching the URL field for https://www.ncbi.nlm.nih.gov/pubmed/ and replacing with https://pubmed.ncbi.nlm.nih.gov/ . The PubMed import filter has been updated to use the new URL prefix for newly imported references.
Importing from PubMed by dropping a URL on the library window has been updated to work with the new PubMed servers
Bookends will treat *.md (markdown) files as text files for the purpose of scanning
Increased constraints on Google Scholar searches. This should decrease the chances that frequent searches will trigger Google Scholar's robot detector and block your access.
Folder names are sorted alphabetically when using a right-click to add groups to a folder
Improvements in the arXiv parser. The tags primary_category and category will be listed in the summary pane. You can edit the arXiv import filter to import them into the fields of your choice.
If you invoke a smart SQL group containing invalid syntax, Bookends will send you a notification with the diagnostic information rather than a modal dialog
Database engine updated
Bug fixes:
Fixed a bug where the top of the reference list could obscure the PDF toolbar in full screen view. Fixed two bug where the text in bibliographies generated for Nisus Write Pro or saved directly to disk as RTF was in Dark Mode was white. Fixed an issue with some imports from JSTOR where titles were truncated if they contained a quote mark. Improved trapping (ignoring) of invalid entries in the Quick Add dialog. Bookends will now work if you mistakenly remove the live search field from the toolbar. Fixed a bug in cloud sync that could prevent the library from being opened with a "record locked" error message. Fixed a bug in the reference list view where the sort after pressing the header was not in the correct direction. Fixed a bug in editing or copying of notecards where some characters, including smart quote marks and apostrophes, were lost. Fixed an error that occurred when using the keyboard shortcut to go to the PDF find box. Fixed a problem where having the location of cited pages specified in the citation options tab would result in the removal of any text styles if cited pages weren't included in a temp citation. Fixed a problem where some Unicode characters didn't appear in the formatted reference. Fixed a bug when using a menu to move groups to a nested folder where the UI would initially show the groups in the wrong folder. Fixed a bug in wi-fi sync where an error sometimes occurred when syncing a new Mac library with one that existed on the iOS device.

New in Bookends 13.4.1 (May 3, 2020)

Updated the PDF toolbar and added new graphic elements
PDF Table Of Contents: An icon or menu option (Shift-Command-T) in the PDF Action pop-up menu opens the table of contents (TOC) in a popover window. Select an entry (click or use the arrow keys), to go to the corresponding point in the PDF. If an entry contains a destination URL, it will open in your browser.
Right-click on the PDF proxy icon in the PDF toolbar to pop-up a menu listing each folder in the pathname: Select a folder to open it its enclosing folder in the Finder and select it. This works just like the window proxy icons.
Manage continuous PDF highlighting via the keyboard: When a PDF is showing and has the focus, pressing Control-1 through -5 (without the Command key being pressed) will turn on continuous highlighting with the color corresponding to the number. Any text selected when this is done will be highlighted. Pressing the Control key and the same number as the current color will turn off continuous highlighting.
Added a warning dialog when a damaged format is detected: It instructs you to move the damaged format file to the trash and select another.
There is a separate Dark Mode setting for the color required BibTeX fields in preferences
The list selection color is now the macOS accent color: This requires macOS 14 (Mojave) or later. For High Sierra the selection color is blue, as was previously the case.
Updated Bookends Browser import from JSTOR and WorldCat to deal with changes made by these sources
Improved detection of PDFs in some web pages
There is an option to hide group pane folder badges: Right-click or use the group action pop-up menu to show (default) or hide the badges that tell you how many items are in a folder.
Newly created scanned files will have the word "scanned" instead of "formatted" in their names
Preference settings for openURL will be synced between computers
Bug fixes:
Fixed a problem where the top of the library window could appear offscreen. Removed extraneous HTML from the Abstract of Google Scholar results when sorting by date. Many fixes for cosmetic issues in Dark Mode. Fixed a bug where bibliographies created for Mellel in Dark Mode were white. Fixed a bug in the generation of formatted citation examples. Fixed a bug in the height of the PDF in the edit pane's Attachment tab. Fixed a problem where some users weren't able to select options in the Inspector's segmented button. Fixed a bug that caused errors when opening libraries after customizing some of the toolbar elements. Fixed a bug where styled text changes weren't saved in dark mode. Fixed a bug in the automated PubMed search window where selected a library from a number that are open failed to import the references. Bug fixes for Wi-Fi sync. Fixed a bug that prevented Autofill From Internet from working with ISBNs. Fixed a bug in Remove Duplicates that prevented changes made in the Verify process from being saved. Tool tips for the buttons in the library window bottom strip were restored. Fixed an issue where the selection could change in the reference list after doing an Autofill From Internet. Fixed several instances where changes in the database weren't synced. Fixed a bug where bibliographies created by scanning a Pages files in Dark Mode where output in white instead of black. Restored the dialog asking you to paste in the bibliography after a Pages scan.

New in Bookends 13.4 (May 3, 2020)

Bookends is Dark Mode compatible: There are a few minor changes in the UI to make the appearance work well in light and dark mode.
The library window now has a macOS-native toolbar: This means that you can use a right click to configure the toolbar as you like. The only control that can't be removed is the live search field.
Detach attachments in the Inspector by pressing the Delete key: Menu items available in the old Action pop-up are now available with a right-click.
The Google Scholar and arXiv search results can be returned ordered by relevance or date
You can select multiple citations at once in the floating citations window: This makes it possible to perform operations like Copy Citation on several references at once to create a citation group.
The Links column in the library window is updated immediately when links are added or removed
Improved SQL search: Newly created or edited SQL searches will be checked for validity before the dialog is closed. If there is an error the dialog will remain open so that you can fix the problem and try again. The group pane hierarchical menu will offer to edit a saved SQL search rather than rename it.
Duplicate a smart group with a right-click or the Groups Action pop-up menu
Delete terms from the library with a right-click in the Term List window
Scanning of Apple Pages has been updated to work with Pages version 10
Import References from the Online Search window with File -> Import References -> Import Selected References (Shift-Command-I)
Amazon France and Amazon Germany searches have been removed: These sites finally caught up with Amazon.com and began throttling searches, rendering them useless for Bookends.
Updated database engine
Bug fixes:
Fixed a bug where the default output style was set to Styled Text after scanning a Word document regardless of the setting in preferences. Fixed a bug where removal of attachments in the Inspector wasn't marked for sync. Fixed a problem with an atypically-encoded en dash in an ISBN used in Quick Add. Fixed a bug where a duplicated reference wasn't automatically added to the original's group, if any. Fixed a bug in where the short title created from the full title via a right-click wasn't saved. Fixed a bug in opening and displaying attached Mellel files. FIxed several issues with the Watch folder. Fixed an error in Bookends Browser caused by missing data returned from CrossRef. Fixed a bug where the Import Reference menu was enabled inappropriately.

New in Bookends 13.3.2 (Feb 23, 2020)

New in Bookends 13.3.1 (Feb 11, 2020)

Bookends Browser has been completely rewritten: Bookends Browser now uses a more modern macOS API that has many advantages, including faster page loading, much better compatibility with web sites using complex Javascript, no interference by the Adobe PDF plug-ins, the ability to display webarchives, and fixes a problem some people had with logging into iCloud to use sync. One feature has been removed: automatic fill-in of login name and password is no longer available.
The warning about the presence of Adobe PDF plug-ins has been removed because they no longer interfere with Bookends (see above)
Much improved importing from Papers 3: Bookends will now import reference citekeys and manual collections from Paper 3. Limitations: (1) collection hierarchies will not be preserved (i.e. the manual collections will be converted to Bookends static groups at the top level), and (2) if you have nested manual collections, the references will be imported into a single static group that has the name of the topmost collection.
Enable/disable EZProxy while in Bookends Browser: Click on the bookmark icon to use EZProxy to access web information. Bookends will use the preference settings for the EZProxy address. If there are none entered, you will be asked to provide the information in Bookends Browser. This is handy if you want to mix searches that do and do not go through your university's authentication servers.
Various enhancements and fixes were made to the reference list in the library window
In addition, the dates added and modified are now shown in the form YYYY-MM-DD + time.
Updated database engine
Bookends will import a reference if its URL from the updated PubMed web site is dropped onto the library window
The base URL of this site is "https://pubmed.ncbi.nlm.nih.gov".
Bug fixes:
Fixed a bug in citation disambiguation when scanning with an author-date format. Fixed a bug that prevented direct import from Google Scholar if you are using EZProxy. Fixed a bug in Standardize Journal Names. Fixed a bug in the tag cloud search for authors and editors that have periods after initials. When changing a selection in the tag cloud any text in the live search field will be taken into account in filtering references. Fixed a bug in the Links Inspector where clicking on an empty row would deselect all references in the library window. Hyperlinks to unique IDs in the Summary view will only be created if the # in the abstract or notes is followed by a number.

New in Bookends 13.3 (Jan 6, 2020)

Improved detection of the correct URL for a reference in a Google Scholar web page
Formatting references as BibTeX is much faster
Direct import from Papers 3 will work even if Papers isn't running
Updated "Import From Existing Bibliography" to deal with changes made by CrossRef
The super- and subscript metacharacters will be removed from the title when submitting an OpenURL search
Updated the JSTOR import with Bookends Browser to deal with changes made by JSTOR
Renamed Live Search option from "Spotlight" to "Attachments (Spotlight)" to make this search capability clearerImproved DOI detection in web pagesAdded the ability to detect and automatically download PDFs from several chemistry journals and the ACM Digital Library
Updates for Catalina:
Fixed a problem where some default fonts, such as Times New Roman, weren't recognized as such and were substituted with Helvetica in formatted references. Fixed an issue where the style of literal text in a format (e.g. bold) was not carried through to the formatted reference. Fixed a problem when clicking on PDF text that was highlighted in Papers 3. Fixed a hard crash that occurred when formatting thousands of references as BibTeX.
Import from Google Scholar in Bookends Browser:
This feature requires that Google Scholar is configured to export citation information, which is indicated by a link below each reference with the words "Import into" followed by a destination, If you do not see this, use Bookends Browser to go to Google Scholar and click on the preferences icon (3 horizontal bars at the upper left, and then either the word Settings or the gear icon). Check the option to "Show links to import citations into" and select RefMan (preferred), EndNote, or BibTeX as the destinations from the pop-up menu. When you subsequently use Bookends Browser to search Google Scholar, each result will have the link "Import Into Bookends". Click it to import the reference into the frontmost Bookends library. Sometimes Google Scholar has the URL of the PDF. If so, and you have access privileges to the PDF, it will be automatically downloaded.
Reference metadata will be imported from a direct search of Google Scholar even if Google thinks you are a robot:
In this case the data are scraped from the web page and may not be complete.
Sort groups and folders:
Right-click on the groups pane or use the groups pane Action pop-up menu and select "Sort Groups". All groups and folders, including their contents, will be sorted alphabetically.
Finding and displaying attachments is up to 3 times faster:
This will be noticeable when you have many attachments.
New Library of Congress online search:
The new search is UTF-8 compliant, meaning that non-Roman (e.g. accented) characters will be returned correctly.
Updated detection and removal of the Adobe PDF Viewer plug-ins:
These plug-ins (AdobePDFViewer.plugin and AdobePDFViewerNPAPI.plugin) can cause serious problems when displaying or downloading PDFs in Bookends Browser. Because of increasingly stringent security protections implemented by Apple, Bookends can no longer remove them for you. If detected, Bookends will alert you and offer to show them in the Finder. You can then either trash them or remove them from the Internet Plug-ins folder.
Bookends no longer scans documents created with Pages '09 or earlier:
Refs -> Scan Open Apple Pages Document will not be enabled unless a more recent version of Pages, version 5 or later, is running.
PDFs added from the watch folder will not be renamed if their metadata is not found online:
You can now tell Bookends to "Rename imported files if metadata are found" in the Configure window. This is the reverse of the previous setting, which was "Don't rename imported file".
Automatic import of reference from files with uniquely identifying extensions:
If you drop a file that has an unambiguous identifying extension Bookends will import the references without asking which filter to use. This applies to files sent to Bookends by other applications, like Firefox, as well. The extensions Bookends recognizes are .ris, .bib, .nbib, .enw, and .ciw. In such cases the current settings for adding the imported references to the Hits List, and if the file should be moved to the Trash, will be used. To change these, use File -> Import References and the configurable import dialog will appear. Import dialog settings are saved even if you cancel the import.
Simple arXiv searches are by word:
This means that if you search for "solar eclipse", references that contain both words will be found, even if they aren't in that order. Boolean searches will continue to search by phrase.
Updated database engine:
Fixed a bug that caused a crash when using "cast" in an SQL group.
Bug fixes:
Fixed a bug that prevented the creation of PDF comments. Fixed a bug in the Summary view where extra returns were added around styled characters in the abstract or notes and par would be shown in place of returns. Fixed a bug that prevented styled text information added when editing a notecard to be saved. Fixed a bug that prevented the Browse button in the Attachment dialog from setting the pop-up menu to the selected subfolder. Fixed several bugs in opening of spring loaded group folders. Fixed a bug that could prevent some PDF DOIs from being resolved. Fixed a bug that prevented the last PDF highlight from appearing in the note stream. Fixed a bug in Wi-Fi sync. Fixed an issue that will make importing direct importing of references from Papers 3 more reliable.

New in Bookends 13.2.8 (Dec 2, 2019)

New in Bookends 13.2.7 (Oct 27, 2019)

Catalina compatibility fixes: Opening PDFs in a non-default app works. Scanning an open Apple Pages document works even when Bookends is not given Full Disk Access. Searching for DOIs in certain PDFs when attaching no longer causes a crash.
When file renaming is done using a format, Bookends will make sure only one period precedes the extension
Bookends can perform BibTeX scans on files with the extension .tex
Changed the keyboard shortcut for "Make Quoted PDF Highlight From Selection" to Control-Shift-Command-Q. The old shortcut, Control-Command-Q, is now used by macOS to lock the screen.
Added a keyboard shortcut for Sync Now: Control-Command-S
A trailing return will be removed when performing Copy Formatted
Improved JSTOR URL detection of older URL schemes when attaching PDFs
Identification of invalid DOIs in web pages is much faster
Only straight quote marks will be output when generating HTML-formatted references
Bug fixes:
Fixed a bug where a file's extension was repeated when it was automatically renamed. Fixed a bug that caused an error when doing a file tag search and there were no hits. Fixed a bug where there would be a long delay when trying to access a server that is no longer mounted. Fixed a bug where the attachment pane wasn't updated properly when displaying a text or rtf file. Fixed a bug in Window -> Reset Position where the tops of the Format and Import Filters Manager would be offscreen. Fixed a problem where on occasion the word processor wasn't returned to the front after a scan. Fixed a bug in Find where references could be found and made hits when doing a search for both text and Spotlight when the latter found no matches. Fixed a bug in creating a new standalone reference window when that preference option was selected. Fixed a bug where the author/editor capitalization rules could be ignored if there was no first name and the output was surname last. Fixed a bug in the concise view where the coloring of a file tag was offset by 2 characters. Fixed a bug that caused unnecessary updating of database fields. Fixed a bug that could cause an error when syncing references for which an attachment was modified. Fixed a problem in syncing of groups with iOS when the parent folders have non-Roman names. Fixed a bug in the attachments inspector where the contents of an attached textual (non-image) file wasn't refreshed properly. Fixed a bug that could corrupt a format when the "repeated authors" field was updated. Fixed an issue in HTML markup where replacing a < with its HTML entity prevented the creation of hypertext links. Fixed a bug in the display of attached Mellel documents containing images.

New in Bookends 13.2.6 (Sep 15, 2019)

Updated the JSTOR importing function to deal with changes made by JSTOR
In addition, when JSTOR provides editors names Bookends will import them.
Updated parsing of Google Scholar URLs to deal with changes made by Google
When you launch Bookends and there's a second copy of Bookends on the network, you will be offered the choice of quitting the remote copy, in which case you can continue to work on the local machine, or the local copy
Previously you had to quit the local copy.
Bookends will include qualifiers when importing PubMed MESH headings (keywords)
Updated database engine
You can permanently remove references from the library itself when in a group, virtual group, or folder by holding down the Shift key when you Delete
Right-clicking an image (not a PDF, which has its own Action pop-up menu option) in the display pane or Attachment tab of the edit pane will offer to Move it to the Trash.
This is in addition to Detach, Zoom In, and Zoom Out.
Backward compatibility
Bookends will no longer convert formats made for, or import files exported from, versions prior to 11.2. Bookends won't offer to convert libraries made with versions 8 or earlier. Bookends no longer creates a special folder to store custom formats made with Bookends 11 or earlier.
BibTeX scans will recognize complex citations where modifying instructions are inserted between the citation beginning and the cite key, such as citep[see][chap.~2]{smoth2019}
Note that if you are having Bookends insert final citations when you scan, the modifying instructions will be ignored.
Mellel will be brought back to the front after the verifying references process has completed
When attaching a PDF Bookends will look for its DOI on the second page if there is none on the first
When automatically renaming PDFs slashes (/) will be removed from file names
Slashes are allowed in macOS but not iOS.
Bug fixes:
Fixed a bug when adding a PDF via the watch folder to an existing reference where it would replace any attachments already there. Fixed a problem where Bookends wouldn't recognize temporary citations in Scrivener footnotes. Fixed a bug where Bookends couldn't find a file inside an attached folder. Prevented an error that could occur when closing the Online Search window when a browser search was in progress. Fixed a bug in the Links Inspector where the comment field was locked when it should be editable. Fixed a bug that could cause text to become temporarily invisible when coloring required BibTeX fields. Fixed a bug where no field got the focus when exiting the Key field while BibTeX citekey duplicate checking is enabled. Fixed a bug in renaming attachments where Bookends would use a space before a random number even when the user asked for underscores in preferences. Fixed an error that could occur when trying to import metadata for some references from CrossRef. Fixed a problem when using tag cloud file tags and the PDF name included a slash. Fixed a hard crash that could occur when closing the library window after using tag cloud file tags. Fixed problems in the Compare References window where changes in the marked or ratings status of references weren't being updated in the database of the UI. Fixed a problem when doing an Autofill From Internet for multiple references at once via PubMed where references weren't updated. Fixed a bug in AppleEvents that could cause a search of some SQL groups to always return 0 references.

New in Bookends 13.2.5 (Jul 20, 2019)

PDFs can be downloaded automatically from more journals
Updated database engine
Bibliographies in Word can contain colored text
The "show thumbnails" setting in the PDF viewer will stick when moving between references that do and don't have PDF attachments
Bookends will move a format file to the Custom Formats folder and enable it for you when you drop it on a library window or double click on it
When using Biblio-> Bibliography and sending the output directly to disk, the suggested file name will include the name of the format (e.g. Bibliography (Turabian).rtf"
Bookends code is hardened and notarized:
This is in preparation for the upcoming macOS 10.15 (Catalina).
Embed links to web pages in formatted references:
This is controlled by the format by the use of < and > punctuation – see the section on formatting in the User Guide for details. Embedding links to external web pages works with Microsoft Word 2016 (version 15.x) or later and Nisus Writer Pro. It does not work with Mellel at this time. It will not work with Pages or LibreOffice.
Global Change -> Standardize Journal Names:
This option is enabled if you are using a journal glossary. You can choose to have all journal names found in the glossary be changed to the short name (e.g. J. Biol. Chem.) or the full name (e.g. Journal of Biological Chemistry), and/or have periods removed (e.g. J Biol Chem). It is not necessary to have the same journal name be identical in all corresponding references because the glossary will substitute the required form at the time of formatting. However, some users want uniformity in the library itself and in the Journal Term List.
Refs -> OpenURL Search will display the results in the library window browser view (lower pane):
This makes it easier to click through links to a PDF and then attach it to the reference. Previously Bookends opened the results in an external browser.
Bug fixes:
Fixed a bug in full screen view where the live search field showed inappropriately when a PDF was on display. Fixed a bug where the PDF lock icon could be shown when the PDF was not locked. Fixed a bug that prevented scanning of BibTeX citations. Fixed a bug when using smart caps SURNAME for formatting. Fixed a bug in QuickAdd that caused searches for ISBNs with hyphens to fail. Fixed a bug that caused hanging indent settings to be ignored when the bibliography contained colored text. Fixed a bug in which the OK button was not enabled when renaming a static group. Fixed a bug in deleting references from a group where Bookends would mistakenly offer to delete them from the library. Fixed a crash in Bookends Browser when checking DOIs with CrossRef. Fixed a bug that could cause an error when searching for a unique id in the Find window.

New in Bookends 13.2.4 (Jun 24, 2019)

Added a workaround for problems caused by some anti-virus software when creating a new library
Most Amazon search sites (including Amazon.com) have been removed:
Amazon is enforcing a new policy that reduces (throttles) the number of searches that can be performed over a period of time based on the number of sales generated. Because Bookends uses Amazon for obtaining metadata, not referral for sales, this means that Bookends is effectively prevented from using Amazon as a source of metadata. Amazon.de and Amazon.fr are working as before for now and remain. If/when they stop working they will be removed, too.
Google Books is added as source of book metadata when using an ISBN with Quick Add and Autofill From Internet:
You can choose between it and Amazon (France) and Amazon (Germany) as your preferred source in preferences, Internet tab. If an ISBN isn't found at the preferred source Bookends will query the other sources until it succeeds or the ISBN can't be found.
Added an AppleEvent that will will return the file path of the default attachments folder:
This is useful if you want to use AppleScripts to add attachments to references and need to move the files to the default folder.
When launching Bookends after a crash the user will be asked if he wants to open the last-used library:
This prevents an endless cycle of crashes if a corrupted library is at fault. Previously, the library would not open automatically after a crash and the user would have to use the Open -> Recent menu to use it.
A lock icon will appear when viewing read-only PDFs and the annotation tools will be disabled:
Click on the lock icon to have Bookends unlock the PDF by assigning read/write permissions to the PDF.
Bug fixes:
Fixed a bug that could cause the Types and Labels preferences to be reset to the factory default when updating to a new version when cloud sync is not enabled. Fixed a bug that could cause text to be invisible in the edit pane when using BibTeX and indicating required fields with color. Fixed a bug in the replacement of an older Word .dotm file with a newer version. Fixed a bug that prevented Bookends from telling you that you can't remove a reference from a smart group with the Delete key. Fixed a bug in handling of the AppleScript command to get the selected references. The PDF highlight marker color updates immediately when the user selects a different one. Fixed several wi-fi sync bugs involving groups. Fixed a bug in cloud sync. Fixed a bug that prevented Bookends from fetching and syncing the PMCID.

New in Bookends 13.2.3 (May 26, 2019)

New in Bookends 13.2.2 (May 12, 2019)

Updated direct download of PDFs from ScienceDirect to deal with changes made by Elsevier
Updated PubMed web viewer to deal with changes made by PubMed
Perform boolean Spotlight searches for phrases (i.e. text enclosed by quote marks)
Live search for text between quote marks now searches for whole words
New citation delimiter option: (+ +)
Some global preference settings will be synced via the Cloud:
The synced settings are: the default reference Type (Mac and iOS), the names of reference Types and field labels (Mac and iOS), the temporary citation delimiter (Mac and iOS) and separator (Mac), the EZProxy URL (Mac and iOS), super- and subscript metacharacters (Mac), the floating citations trigger key (Mac), and author and title ignore lists (Mac). We will add more global preference settings in future updates. Use of synced preferences by Bookends for iOS requires version 3.3.6 or later.
Modernized Bookends options in the ribbon for Word 2016 or later/Office 365:
The macros that interact with Bookends now appear in their own tab, the Add-ins tab is no longer used.
The menu Refs -> Mark Selected References toggles the marked (hit) status of the selected references:
If the first selected reference is unmarked, all selected references will be marked. If it is marked, all selected references will be unmarked.
Bug fixes:
Fixed a bug that could make the library window invisible. Fixed a problem on systems running anti-virus software where the Types and field labels reverted to the factory defaults. Fixed a hang that could happen when highlighting a reference's owning groups and one of the groups was not visible. Fixed a bug that prevented the pop-up menu listing all attachments from appearing at the bottom of the Attachments tab in the reference edit pane. Fixed a bug in Reset Window Position where the library window wasn't the full screen height. Fixed a bug in the display of en dashes in the Format Manager examples and of en dash display in scanned Mellel files. Fixed a bug that could cause PDF tags to overlap when viewed in the Attachments tab. Fixed a bug that could cause an error when saving an edited format. Fixed an issue with Bookends Server where the default formSat was used to generate a bibliography even though a different format was requested. Fixed several bugs in coloring of required BibTeX fields. Fixed a bug that prevented italicized numeric citations from displaying in a scanned Mellel document. Fixed a bug in the registration window display of dates for some countries where the day rather than the month appeared. Fixed a bug where Refs -> Replicate As Book Chapter -> Include Attachments was enabled inappropriately.

New in Bookends 13.2.1 (Mar 31, 2019)

A new AppleEvent lets you get the selected references in the library window
Example Applescript: set myRefs to selected publication items of front library window.
Restrict PubMed searches to articles for which the PDFs are free for you
The references that are free for you may depend on your current IP address and may differ in different locations (e.g. work vs. home). This setting in the Online Search window applies to both normal and advanced PubMed searches.
Automatic detection and removal of the Adobe PDF Viewer plug-ins
Adobe products can install two plug-ins that provide their own tools for viewing PDFs in browsers such as Safari. These plug-ins are incompatible with Bookends and can result in faulty PDF displays, failure to download PDFs, and even crashes. When you open Bookends Browser or activate Autocomplete Paper, Bookends will check for the presence of these plug-ins and, if found, offer to remove them. If you accept, Bookends will move the plug-ins to the Trash. If you don't accept, Bookends will allow you to proceed but warn you again the next time you run Bookends. Note that removing these plug-ins will have no effect on Adobe Acrobat or Reader.
Set the font size for groups and the note stream in preferences
The font face is not configurable.
When entering a PDF tag, pressing Return or Enter accepts the tag
Pressing Tab accepts the tag and places the cursor in a new empty tag field so you can enter another.
Copy Notecard And Citation will place the plain as well as the styled text in the clipboard because some apps only recognize the former
The reference list sort is by first column then title if there is no date column
As before, if there is a date column the sort is by first column/date column/title column.
Faster population of fields in the reference edit pane
Use the keyboard shortcut Shift-Command-M to mark (make hits of) the selected references
Improved UI for changing field labels in preferences
Selecting a row in the Type list automatically fills out the corresponding fields in the field label list.
Online Search of arXiv will retrieve the id and import it to the pages field
A slightly darker yellow will be used for groups that are selected when highlighting groups a reference belongs to
Added a delay in automated PubMed searches with multiple queries to deal with new restrictions imposed by PubMed
Bug fixes:
Fixed a bug that prevented hypertext links into Bookends from other apps and the browser bookmarklet from working. Fixed a bug in adding text to a reference via AppleEvents. Fixed a cosmetic bug where the progress window didn't update properly when removing orphaned attachments or exporting references as XML. Fixed a bug in Autocomplete Paper from arXiv. Fixed a bug where the contents of the Notes field were not completely removed when moving from one reference to another. Fixed an error that could occur in Online Search when switching too quickly between references found on Google Scholar. Fixed a bug in Wi-Fi sync. Fixed a bug that prevented saving import filter searches. Fixed a bug that caused a right-click on an import filter saved search to fill out the search fields. The online source icon updates properly when a new site is selected. Fixed a bug in a Google Books search where the cover art display wasn't updated when there was no picture. Fixed a bug that prevented Autofill from importing text to a field that already contained styled text. Fixed a problem with some Japanese Word documents where the ending number of a citation span wasn't output. Fixed a bug in floating citations where dragging a row would actually drag the entire window. Fixed a bug in citekey generation that would cause a disambiguating letter to be inappropriately added. Fixed a bug that caused PDF tags to overlap when the library window opened with the PDF pane showing.

New in Bookends 13.2.0 (Feb 21, 2019)

Bookends is AppleScript-able. Bookends has an AppleScript dictionary with properties and commands that let you retrieve and set reference metadata, add and populate groups, fetch formatted references, and more. See the User Guide for details. Note that this supersedes the previous AppleScript mechanism, which is no longer under development but is retained for backward compatibility.
Place cited pages inside a final citation. In previous versions Cited Pages were always placed at the end of the final citation. Now, however, you can insert them anywhere in a custom format by placing the @ character in the Field Order field where you want them to go. For example, if you create a format with the order a. t. @ (d). Bookends will replace the @ with the Cited Pages you have enter in the temp citation. Bookends will add any pre- and post-characters specified for Cited Pages in the format definition (for example, "p. " and " "). Using the example above this might be output as: author. title p. 12 (2019). If you use such a format and do not specify Cited Pages in the temporary citation, the @ character will be removed in the final output. Note that when you use such a format outside of scanning (i.e. it is not possible to add Cited Pages), the @ will be replaced by @@ to indicate where the Cited Pages would be placed when provided.
The format symbol for Unique ID has been changed to = (was @, which is now used for Cited Pages)
Continuously highlight a reference's owning groups. If this option is selected in preferences (Lists tab), Bookends will always highlight in yellow any groups to which the selected reference belongs. The default option is to show such groups only when Option-Shift is pressed.
Updated importing from JSTOR to deal with changes made by JSTOR
Cloud sync will be halted and the user notified if Bookends detects that the library file is in a file sync folder (e.g. Dropbox, iCloud Drive, or Google Drive)
Combining Bookends cloud sync (which updates just the metadata that have changed) and file sync (which uploads/downloads the entire library) can cause problems. The solution is to move the library file to another folder (the Bookends default is ~/Library/Application Support/Bookends).
Added the option to create temporary citations as Author, Date, PMID
This may be useful to those in biomedical professions who are writing papers with collaborators using EndNote, which should recognize these citations. If a reference does not have a PMID entered the Author and Date will be used.
Bookends will replace a / with a - if necessary when naming a library for sync on iCloud Drive
Added Shift-Command-L keyboard shortcut for Copy Hypertext Link in the floating citations window
The Pages script "Find in Bookends" has been removed because Apple Pages no longer supports this AppleEvent functionality
If the recently viewed list is corrupted, Bookends will empty it rather than generating an error that prevents the library from being opened
Added an option that tells the Watch Folder to leave an attachment's name as is when moving or copying it to the default attachment folder
This setting is in the Watch Folder -> Configure window.
Formatting a reference that has a field with an unclosed superscript or subscript will no longer cause the baseline of all subsequent references to be affected
Bookends Browser should now load URLs that contain accented (Unicode) characters
Added @conference as a valid BibTeX reference Type
Slashes (/) are not allowed when renaming attachments. Slashes are not allowed in iOS file names
If Bookends can't display an attachment it will suggest you double click on the (empty) display pane to open it in a compatible app, if available
You can now import the Epub date from PubMed by using the tag DEP in the import filter
You can email references and attachments via the Airmail app
Bug fixes:
Fixed a bug in Mellel scans where the & metacharacter was removed during a Verify and the instruction (exclude authors and title) ignored. Fixed bugs that would cause the focus to move to the reference list after editing keywords and move to the authors field when clicking out of live search box to an editable field. Fixed a bug that incorrectly recreated the formatted view if the reference was edited while that display pane was open. Fixed a bug where citekeys generated by Bookends might not sync via the cloud. Fixed a situation where the floating citation window could be off screen if it had been used on a second monitor that was then disconnected. Fixed a bug that would cause a malformed final citation group when the author was being placed in front and the format sorted the citation group. Fixed a bug in Sente XML import where the first character of a comment could omitted. Fixed a bug that could cause the Online Search window to appear more than once in the Windows menu. Fixed a bug in drag-reordering of groups. Fixed a bug where styled text information in a format's quoted text was ignored when the output was marked up as HTML or BibTeX. Fixed a rare bug in sorting of the reference list. Fixed a bug with saving bibliography generation defaults from the "export formatted references" dialog. Fixed a bug in Quick Add where some valid PMIDs were not found. Worked around a problem where opening a library caused a "-47" error when running antivirus software. Fixed a bug in Option-Shift group highlighting where the wrong item would be highlighted if a preceding folder was opened and then closed. Fixed a bug in cloud sync where spurious references could be added to the library. Fixed a bug in Mellel Synchronize Databases where references would be imported from a document even if they were already in your library. Fixed a rare error that could occur when saving text from the concise view field.

New in Bookends 13.1.5 (Dec 19, 2018)

Updated database engine
Bookends will display Google's reCAPTCHA page when Google Scholar thinks you are a web robot
Google Scholar will sometimes think you're a web robot based upon your search and downloading activity and refuse further service. If this happens when you're searching in the Online Search window, Bookends will show the Google confirmation page with a reCAPTCHA asking you to confirm you're not a robot. Once completed your search rights will be restored, although the time this takes is variable and can be up to 24 hours.
When importing malformed XML, Bookends will alert you and show the lines generating the error
This information may help you correct the XML in a text editor or, if exported from another reference manager like Sente or Papers, delete the reference whose metadata is incorrectly represented.
Bookends will prevent duplication of keywords in a reference
Added a "include attachments" option when replicating a reference as a Book Chapter
This is useful, for example, if you have the PDF of the entire book and you want each chapter to have that as an attachment.
Increased the timeout setting for Bookends Server to deal with problems with network latency
HTML-formatting of references has been improved and is now compatible with XHTML
The "generate bibliography" setting in the Scan dialog is remembered throughout a session
It is always "true" when Bookends is relaunched.
The upper limit of references that Bookends will detect on a web page in Bookends Browser has been increased to 100
The menu item "Synced iOS Device Info…" has been renamed "Wi-Fi Synced iOS Devices…", and is disabled if there are none
Quote marks will be removed from PDF names when when they are being automatically renamed by Bookends
Export Attachments is a right-click option if any selected reference has attachments
Previously this function was only available if the first selection had attachments.
Bookends won't show a recently opened library in the Open menu if it was moved to the Trash
Bug fixes:
Fixed a bug in BibTeX export where a close instead of an open smart quote could be output by mistake. Pressing Option when invoking Copy Citation or Copy Formatted copies to the clipboard but no longer switches to a linked word processor. Fixed a bug in EndNote XML import where the URL could be imported into the wrong field. Fixed a rare bug that could cause an error if you changed a field label and then did a live search on that field. Command-+ and Command-- keyboard shortcuts now zoom in or out PDFs displayed in the edit pane's attachment tab. Fixed a bug that prevented Bookends from importing titles beginning with a superscript from PubMed. Fixed a bug where the Hits menu wasn't enabled after a Spotlight live search. Fixed a problem that could occur if a library was a term's corresponding references weren't shown.

New in Bookends 13.1.4 (Oct 15, 2018)

Import references from multiple files at once with drag and drop
If you drag and drop more than one text file onto the library window Bookends will import the references contained in all. Note that the references in each file must be in the same format (e.g. RIS, PubMed, XML, etc.) or some of the references will not be imported. If any of the files is not a text file Bookends will offer to attach them all (the previous behavior).
Styled text information in the Abstract and Notes will be preserved when importing EndNote XML files even if more than one EndNote field is combined
When attaching a PDF to an existing reference that is showing in the list (e.g. in a group), Bookends will not change the group selection to All
Bookends will generate a more useful error notification when the PubMed network connection is dropped
PubMed is having intermittent connection problems that affect some users.
Export PDFs attachments with or without annotations via the File menu or by using a right-click
Copy Hypertext Links from the floating citations window
Note that many apps, including Word, do not accept hypertext links.
The rarely-used non-editable PDF viewer has been removed.
PDFs are now always displayed in the more versatile PDF annotation view.
Improvements were made in the way AppleEvents are handled in macOS 10.14 (Mojave)
Adding terms to references via the Term List window will not bring up a confirmation dialog
A notification will be sent after the terms are added.
The floating citations window height will adjust accordingly if "always show scrollbars" is selected in System Preferences
Bug fixes:
Fixed a bug where some Google Scholar searches could cause an error message. Fixed a bug where the reference edit pane might not scroll back to the top correctly when the window height was increased. Fixed a bug in preferences where the superscript character was shown as = when it was actually set to None. Fixed a scanning error that could occur in some situations when a reference has no author or editor. Fixed a bug that prevented the online search window from showing the references found if a library window was not open. Fixed a bug where pressing Command-+ on some non-US keyboards would not zoom the PDF. Fixed a spurious error that could occur when trying to automatically import metadata from arXiv. Bookends Server Query searches are once again case-insensitive.

New in Bookends 13.1.3 (Sep 10, 2018)

Use floating citations to copy the attached file (PDF) to another application by dragging its icon
The floating citation window will appear when the active application is in full screen mode
The setting "No Enclosing Delimiters" was added to the floating citations window
If checked, when performing a Copy Citation Bookends will not add place citations delimiters (typically curly brackets) around the temporary citation it creates. This setting is saved between launches, and may be useful to some people using BibTeX who create the required citation delimiters themselves and simply want the cite key to be inserted.
Updated the JSTOR parser to deal with changes made by JSTOR
Add arXiv references with QuickAdd. The arXiv id must be entered in the form: arxiv: followed by the id. Example: arxiv:astro-ph/0405136
PDFs with newly created annotations will be saved before being exported or emailed
The modifier key used to trigger floating citations has been changed to Control for new installs. If you've already installed Bookends 13.1.2 this must be changed by you in preferences, Scan & Bib tab.
Bug fixes:
Fixed an issue where the modifier keys on the right side of the keyboard could not be used to call up the floating citations window. Fixed a problem where Control-clicking on a reference in the floating citations window did not activate the hierarchical menu. Fixed a problem where a spurious SQL error could be thrown by the floating citation window when working in another application. Fixed a bug that could cause BibTeX imports to hang. Fixed a bug where Shift-Command-O failed to open the attached PDF when in the standalone reference window Attachment tab. Fixed several problems with the display of webarchives in the lower pane. Fixed a bug where after removing duplicates the number of references in the database shown at the bottom of the library window could be incorrect. Fixed a rare problem where a PDF could be duplicated when performing an Autocomplete Paper. Fixed an error message that occurred when Crossref returned a file type of nil. Fixed a bug in import where the wrong Type was assigned if there were multiple possible comma-delimited tag names specified in the import filter. Fixed a crash that could occur when responding to a link sent from Highlights.

New in Bookends 13.1.2 (Aug 25, 2018)

Use floating citations to copy the attached file (PDF) to another application by dragging its icon
The floating citation window will appear when the active application is in full screen mode
Updated the JSTOR parser to deal with changes made by JSTOR
PDFs with newly created annotations will be saved before being exported or emailed
The modifier key used to trigger floating citations has been changed to Control for new installs:
If you've already installed Bookends 13.1.2 this must be changed by you in preferences, Scan & Bib tab.
Add arXiv references with QuickAdd:
The arXiv id must be entered in the form: arxiv: followed by the id. Example: arxiv:astro-ph/0405136
Bug fixes:
Fixed an issue where the modifier keys on the right side of the keyboard could not be used to call up the floating citations window. Fixed a problem where Control-clicking on a reference in the floating citations window did not activate the hierarchical menu. Fixed a problem where a spurious SQL error could be thrown by the floating citation window when working in another application. Fixed a bug that could cause BibTeX imports to hang. Fixed a bug where Shift-Command-O failed to open the attached PDF when in the standalone reference window Attachment tab. Fixed several problems with the display of webarchives in the lower pane. Fixed a bug where after removing duplicates the number of references in the database shown at the bottom of the library window could be incorrect. Fixed a rare problem where a PDF could be duplicated when performing an Autocomplete Paper. Fixed an error message that occurred when Crossref returned a file type of nil. Fixed a bug in import where the wrong Type was assigned if there were multiple possible comma-delimited tag names specified in the import filter. Fixed a crash that could occur when responding to a link sent from Highlights.
The setting "No Enclosing Delimiters" was added to the floating citations window:
If checked, when performing a Copy Citation Bookends will not add place citations delimiters (typically curly brackets) around the temporary citation it creates. This setting is saved between launches, and may be useful to some people using BibTeX who create the required citation delimiters themselves and simply want the cite key to be inserted.

New in Bookends 13.1.2 (Jul 28, 2018)

New in Bookends 13.1.1 (Jul 9, 2018)

Get PDF from arXiv works even if the reference only has the URL for the arXiv abstract, not the PDF
PDFs automatically imported from the watch folder will be attached to an existing reference if the DOI, JSTOR stable URL, or the arXiv ID matches
Proofreading Word documents preserves quoted text and cited pages in the temporary citations
The minimum database cache has been increased to 20 MB
More accented characters were added to the BibTeX conversion table
Display both citation and bibliography styles in the formatted display pane:
The pop-up menu that holds the names of the enabled formats when you "view formatted" has an option to show the bibliography output only (default) or the citation and the bibliography outputs. You can also switch between these options with a right-click in the view formatted display pane itself. The citation output will be shown first, then the bibliography output. This is most useful for displaying custom citations (e.g. Chicago, Turabian, etc.). Superscripted numbers (e.g. Nature format) will be shown without the superscript.
Move references from one static group to another with drag and drop:
If you drag and drop from one static group to another with the Option key held down, Bookends will remove it from the original and add it to the destination (without the Option key the reference would have been copied and exist in both groups). This may be useful in cases where a reference's status changes and you want to move it between mutually exclusive groups, such as Read vs. Unread or In Preparation vs. Published.
Bug fixes:
Fixed an error message that could be thrown if Bookends Browser couldn't parse a web page. Fixed a crash that could occur when autofilling a reference from Amazon and downloading the associated jpg. Fixed a bug that prevented the "Find in PDF" keyboard shortcut (Option-Shift-Command-F) from working. Fixed a bug in Bookends Browser that could cause a spurious error message to be shown. Fixed a rare bug that could cause a blank error dialog to appers when opening preferences. Fixed a error that was generated if the identifying information in the quick add dialog contained spaces. Fixed a bug where scanning a BibTeX file with an empty citation caused the scan to terminate at that point.

New in Bookends 13.1 (Jun 21, 2018)

New in Bookends 13.0.9 (May 14, 2018)

If Automatically Resize is inactive, a PDF's zoom level will be remembered when switching between references
Bookends will import the Status field in a Sente XML file to User19
Option-clicking on the Online Search button forces Bookends to open the Online Search window with Bookends Browser selected
Updated automatic downloading of PDFs from PubMed Central to deal with changes made by PubMed
Updated Open PDF with PDFPen to work with currently shipping versions of PDFPen
Back and Forward commands have been added to the PDF viewer:
This means that you can go back and forth between a link and the location it takes you to in the PDF.
New AppleEvents have been added that let you get and set the contents of multiple reference fields at once, set reference Types, and get the Bookends version number:
Details of how to use these AppleEvents are available in the User Guide.
Window -> Reset Window Position can be applied to any window that appears in the Window menu:
This is useful for those with multiple screens where for some reason a window's title bar may not be visible. For non-library windows the position will be set to the top left of the screen.
Improved determination of PDF page number when creating a notecard:
Bookends will add the page's relative number in the PDF to the page entered for the reference if the latter is the first of a range. If it's a single number, Bookends will assume it's the total page count for the reference and ignore it.
Bug fixes:
Fixed an erroneous error message you could get with reindexing or rebuilding a library. Fixed a bug when saving an SQL search for the fields Type or Pages. Fixed a problem with automated PubMed search where some searches failed to return any results when they should. Fixed an issue where searching some PDFs for DOIs could result in a crash. Fixed a bug where a PDF in the watch folder could be attached to the wrong reference if the extracted DOI was incorrect. Fixed a bug where locating an attachment that resided on the top mounted volume and not in a subfolder would result in an error. Fixed a bug in Term Lists where after a drag and drop all items would be pinned. Fixed a bug in the Unmatched Citation window where clicking Go To Ref would show the wrong reference. Fixed a regression introduced in the last update that could cause Bookends to hang on launch if it couldn't find a previously-used server.

New in Bookends 13.0.8 (Apr 15, 2018)

URLs imported from Amazon will be shortened to the minimum necessary length
Finding orphaned attachments is considerably faster
Updated import from Amazon Japan to deal with changes made by Amazon
A new preference option that tells Bookends to ignore a double click on a reference has been added
PDF page display settings (e.g. single page vs. two pages) are remembered when switching between references
Updated the JSTOR parser to deal with changes made by JSTOR
Bookends will import the year posted on arXiv if the reference has no date of publication
Copy has been added to the View Formatted contextual menu
When formatting Bookends will use the capitalization rules dictated by the preferred language setting in System Preferences -> Language & Region
Updated database engine:
Note that you must now use quote marks (" ") rather than square brackets ( [ ] ) when performing an SQL search for the fields "type" and "pages" or you'll get an error.
You will be notified if a PDF you are attaching already has a matching reference in the library:
Bookends uses a DOI, JSTOR stable URL, or arXiv id in the PDF to determine if the reference is in your library.
Improved determination of PDF page number when creating a notecard:
Bookends will add the page's relative number in the PDF to the page entered for the reference if the latter is the first of a range. If it's a single number, Bookends will assume it's the total page count for the reference and ignore it.
A number of free OpenURL servers will be be installed in preferences when Bookends is first run:
If you have already run Bookends, you can find the server information for these services in the User Guide and enter them yourself in preferences (Metadata tab).
Change an Inspector parent by double clicking on a reference:
This applies only when the Inspector has a parent reference (i.e., the Links and Cited Inspectors).
Bug fixes:
Fixed a bug in the Attachment Inspector where the Action pop-up Open menu selection did not work. Prevented a situation where an empty attachment name caused an error to be thrown. Fixed a bug that caused an error to be thrown when canceling the conversion of an older library to the current schema. Fixed a bug where having an en dash in an ISBN while doing a QuickAdd would cause an error. Fixed a problem with sync of recently viewed reference data. Fixed a bug in importing of keywords from Google Books. Fixed a bug where the library window wasn't being repositioned when only a few pixels were showing at the right edge of the screen. Fixed a bug introduced in 13.0.7 where clicking on a reference after a Rebuild would cause an error message to be shown. Fixed a bug in dragging references where it could take a long time to assemble the drag information if you have many attachments. Fixed a bug where names imported from Amazon (China) were sometimes improperly parsed. Fixed a problem where a parsing error would occur when evaluating replies from Crossref.org. Fixed a bug in the PDF viewer where the page number could stop updating. Fixed a bug where the default PDF reader selected in preferences was ignored when using Shift-Command-O to open the PDF in the lower display pane.

New in Bookends 13.0.7 (Mar 26, 2018)

Made changes in JSTOR parsing to deal with changes made by JSTOR
Made changes to PubMed searches so that you can retrieve 500 or more references in a search
Updated automated PDF downloads from ScienceDirect to deal with changes made by Elsevier
Refs -> Replicate As Book Chapter will be enabled for references with a user-defined Type
It's up to the user to determine if this is a meaningful option for that Type.
Autofill from Internet will merge existing notes with any imported notes
Bookends will remove spaces before semicolons in formatted references
Cloud Sync normalizes times zones when determining modification dates
Improved Wi-Fi sync:
To decrease the time it takes to sync, Wi-Fi sync will no longer check for orphaned attachments each time it is performed. If heretofore unfound local attachments are can now be found (e.g., they were relocated, or the maximum sync size of attachments was changed), click on the gear icon in the sync window and select “Check for orphaned attachments”.
Recently Viewed group:
This is a permanent group that displays the references you have viewed in descending order (i.e. most recent being at the top). A reference is added to this group if you click on it or a PDF tab and the selection remains showing for a specified interval. In preferences (List tab) you can tell Bookends how long to wait after a click to consider the reference as "viewed", and the maximum number of references to keep in this group. When the maximum is reached the oldest reference will be removed when a new one is added. Clicking on a reference while viewing this group will make it the most recently viewed, but to avoid confusion the list won't redraw until the Recently Viewed group is selected again. If you are using cloud sync, the Recently Viewed group will be synced between Macs but not iOS devices.
Import metadata from PubMed with some style information:
If text is super- or subscripted, Bookends will surround it with the corresponding metacharacters used in Bookends to denote these, otherwise the style information (e.g. italics) is removed. Note that due to limitations in PubMed a space before or after the styled text may be missing.
Bug fixes:
Fixed a bug in the import filter Source parser that prevented some metadata from being imported. Fixed a bug where the setting for using an underscore for spaces when renaming PDFs was not shown properly when preferences was opened. Fixed a rare problem with Mellel Live Bibliography where inserting the same citation multiple times could cause an error to be thrown. Fixed a problem in Bookends Browser where an invalid DOI on the web page could cause an error to be thrown when clicking on the downward arrow icon. Fixed a problem in references found on PubMed where the title or abstract was truncated if style information was included. Fixed a problem where an error was thown when displaying references with no titles for import in Bookends Browser. Fixed a bug in finding and attaching a local PDF when there was a single match. Fixed a bug in the Term List live search where the reference metadata was not updated if there were no matching references. Fixed a bug when attaching PDFs in batch where the metadata was not imported even though a DOI was present. Fixed a bug where the reference list's single column heading was incorrect when sorting by Date Added. Fixed a bug in Global Change -> Remove Orphaned Attachments where the affected references were not updated properly and marked for sync.

New in Bookends 13.0.6 (Feb 19, 2018)

New in Bookends 13.0.5 (Jan 29, 2018)

Scanning is now fully compatible with Word 2016 16.9
PDFs remember their scrolled positions in the Attachments tab (right pane) when switching between references
Drag and drop PDF thumbnails from Preview to the Bookends library window to create a new PDF that will be attached in Bookends
Updated "Print to Bookends" to work in High Sierra
Annotating a PDF will update the date modified field for the corresponding reference in the library
Improved detection of JSTOR stable URLs when attaching a PDF
Each format must have at least one Type:
You will receive a warning if you try to delete all Types.
PDF tabs can be used in the Attachments tab (right pane):
These tabs are independent of PDF tabs in the PDF view in the lower pane.
Improved find and attach of local PDFs:
The search based on the reference metadata is less stringent, resulting in fewer cases where no match is found. Furthermore, rather than always searching the entire drive, you now select the folder (and its subfolders) that Bookends searches for the matching PDF. This decreases search time and reduces the number of spurious matches. Double-click on the full path name to show the PDF in the Finder. There have also been cosmetic improvements in the UI for displaying multiple matches.
• Bug fixes:
Fixed a bug in Rebuild that could cause errors to be thrown after the process was complete. Fixed a bug when using the "Add To Group" menu. Fixed a bug where converting some OpenURL configurations to the new format could result in an error. Fixed a bug that could cause the PDF page count to fail to update when switching between PDFs. Fixed a bug that could cause a mouse click in the PDF toolbar or built-in PDF view to initiate a window drag. Fixed an error that occurred if you clicked on a PDF and then pressed Return. Fixed a bug in rendering PDFs in full screen view on a second monitor and in split-view on any monitor. Fixed a bug where the last sorted heading wasn't remembered if it was the 7th column in the list. Fixed a bug where an & in a group name was not shown in the Add To Group submenu. Fixed a problem where spaces in front or after the reference identifier in Quick Add would cause the search to fail. Fixed a bug in Global Change -> Find and Replace where searching for and/or replacing a Return character did not work. Fixed a bug where clicking a PDF tab wouldn't take you to the reference if the live search field had content. Fixed a bug where exiting full screen PDF viewing by clicking the paper clip icon didn't make the live search box visible. Fixed a bug that could cause some accented characters in a Word document to be misinterpreted during a scan. Fixed a bug that caused an error to be thrown if you tried to edit a reference after Rebuilding the library.

New in Bookends 13.0.3 (Jan 7, 2018)

Automatically import arXiv PDFs when you import the references's metadata.
Quick Look:
Pressing the space bar will display the selected reference's attachments. Press the spacebar again or the Escape key to dismiss the Quick Look display.
Thumbnails of attached files are shown in the single column reference list:
Double click on the thumbnail to open the attachment in your default PDF reader.
Quick Add new references:
If you have a reference's DOI, PMID, ISBN, or JSTOR stable URL you can import its metadata by invoking Quick Add (Refs -> New Reference -> Quick Add or the New pop-up menu icon in the toolbar). Bookends will notify you if you already have the reference. Note that Bookends may not identify the identical reference in your library if the signature information differs (e.g. the ISBN you are looking for has no hyphens but does in your library, or if your library has the ISBN 10 version and you are doing a Quick Add with the ISBN 13 form).
Improved OpenURL:
Each OpenURL server you add in preferences (Internet tab) now has its own name and query parameters. This means that if you have access privileges you can search sites such as Web of Science, Scopus, and Semantic Scholar. You can specify any Bookends field in the query by enclosing the field name in angled brackets, such as < title>. There are two convenience exceptions: < doi> and < pmid> will be mapped to their correct internal names, user17 and user18, respectively. Please see the User Guide for free and commercial OpenURL services you may find useful.
Bug fixes:
Fixed a bug that prevented File -> Export References (Hits) from being enabled if you marked references via the Refs menu. Fixed a bug that sometimes prevented the reference list from being updated when necessary. Fixed a bug in group search. Fixed a bug that could cause a drag in the Online Search window splitter to move the entire window. Fixed a bug in Google Scholar importing where a field's leading quote mark was not imported. Fixed an issue where in some circumstances clicking on an already selected reference would cause its PDF to scroll to the beginning. Fixed several cosmetic bug in the full screen PDF view.

New in Bookends 13.0.2 (Dec 27, 2017)

PDF comments imported from Sente will be separated from the corresponding quote, if any, by an empty line
Changes in cloud sync should result in fewer requests for authentication from Apple
Copy Citation and scanning have been updated to work with Microsoft Word version 16.x
Improved scanning of LibreOffice .odt files
Automated repair of damaged indexes:
If Verify detects a problem with the library, Bookends will reindex it without user intervention. This will result in fewer problems being reported and fewer suggestions to Rebuild.
Updated import from Google Scholar to deal with changes made by Google:
Bookends will import the best information it can obtain from Google Scholar.
Better detection of a linked word processor:
Bookends will now recognize the linked word processor if its name has been changed in the Finder.
Improved scanning of text files:
Bookends will assume the scanned text file has the same encoding as the bibliography output (e.g. plain text, UTF-8, or UTF-16). If the output is incompatible with plain text files (e.g. Styled Text), the text file will be assumed to be encoded as UTF-8.
Click on the Term List header in the library window to filter the list:
This is now analogous to the groups search, except it is "live" (filtering occurs as you type), no need to press Return.
Improved metatag searches:
All searches for metatags are now "by character" exact matches so that they work when tags contain spaces. Note that in the Find dialog the setting of the search type (e.g. "word beginning with") will be ignored if the search term is a metatag.
Bug fixes:
Fixed a bug where Bookends failed to quit when another copy using the same license was running. Fixed a bug where the + button to add a PDF tab was visible in the Attachments pane of the reference edit display. Fixed a bug that prevented PDF page numbers from being updated in the reference edit pane/window. Fixed a bug in the scanning dialog where bibliography output settings as UTF-8 and UTF-16 were not shown correctly. Fixed an error when multiple PDFs were imported into a static group at once. Fixed a bug where the Bookends Browser window was dragged by clicking and holding a toolbar button. Fixed a bug in Author-Date scans where the % and - metacharacters were applied to all citations in a group instead of individual ones. Fixed a drawing artifact caused by opening the PDF pane while working in full screen. Fixed a bug where the buttons in the Inspector window would stop responding to mouse clicks. Fixed a bug where the groups pane might not appear in full screen view if the PDF pane was closed. Removed extraneous commas in the authors names when a reference has more than one institutional author and is displayed in the single column or summary view. Fixed a bug where a right-click would offer to detach an attachment from a reference that had no attachments.

New in Bookends 13.0.1 (Dec 27, 2017)

Bookends does a better job at restoring the original library window pane heights when exiting full screen
Double-click on the PDF proxy icon in the PDF viewer to open it in your default PDF reader
The PDF tabs have been moved to the bottom of the toolbar
The consequence of a reference double click is a preference option:
In preferences (List tab) you can tell Bookends what to do when you double click a reference: open the PDF display pane and add the PDF to the toolbar, or open the reference's edit pane/window.
The PDF toolbar shows the page number:
Click on to bring up a dialog that lets you go to a specific page
Choose your own PDF highlight colors:
In the PDF highlight color selector, Option-click on the color you want to change. To restore a color to the factory default, Shift-Option click on it.
To change the color of an existing highlight, select it and choose a new color from the PDF highlight color selector:
The default highlight color will not be affected.
More flexible handing of repeated citations:
You can tell Bookends to output literal text (e.g. "Ibid.") when a citation is repeated, or to output reference data (e.g. the author). This is determined in the format: Citation Options -> Custom Citation -> Common Settings. The option to output the author when a citation is repeated is used in the new Chicago 17th A format, included in this release.
Open multiple reference windows at once:
If you edit references in a standalone window and each reference opens in a separate window, selecting up to 5 references and pressing Return or Enter will open them all at once.
Import copied text when in Bookends Browser:
If a library is open and you copy text to the clipboard while in Bookends Browser, selecting File -> Import References From File or Clipboard (Shift-Command-I) will bring up the import dialog with the clipboard option selected. Click OK to import to your library.
Bug fixes:
Fixed a bug that could cause an error message when attaching a file. Fixed an error that occurred when using Command-' to copy the Pages information from the previous reference. Fixed a problem with updating of the progress window when doing a Global Change -> Rename Attachments. Fixed a problem where typeahead scrolling didn't work for several lists. Fixed a problem with windows being moved off screen. Fixed a bug where the groups pane would appear under the thumbnail view when viewing a PDF in full screen. Fixed an issue that prevented the Bookends library icon from showing correctly in the Finder. Fixed a bug that could cause a live search error when Label is used as a column. Fixed a bug that would cause an error when doing a BibTeX scan. Fixed a problem in finding attachments in High Sierra when the file named contains a non-breaking space. View -> Edit Reference now brings up the standalone editing window if it is specified in preferences. Fixed a rare bug where in some cases a group wasn’t placed in the parent folder after cloud sync. Fixed a bug that caused an attached jpeg to be shown after another reference was selected.

New in Bookends 12.8.4 (Oct 3, 2017)

New in Bookends 12.8.3 (Aug 21, 2017)

New in Bookends 12.8.2 (Jun 26, 2017)

Show and import references cited by a reference you have:
The Inspector window has a new toggle option Cited By. When selected, the Inspector will use CrossRef to locate the works cited by the selected reference (the parent reference). To change the parent reference, either drag and drop from the reference list onto the Inspector parent reference well, or select another reference in the library and double-click on the Inspector parent reference well. Any that are found will be displayed in a list. References that you already have in your library will have a yellow background -- right-clicking on such a reference will bring up the contextual menu option Show in Library. References that have no DOIs cannot be imported and will be shown with a red background. Double-clicking on a reference that has a DOI will open it in Bookends Browser. An Import button at the top of the Inspector imports the selected references from PubMed if it is available, and if not from CrossRef. Crosslinks will be automatically created for imported references, Work Cited : Work. There are important caveats. First, the reference in your library must have a valid DOI registered with CrossRef. Second, the publisher must have submitted the cited reference metadata to CrossRef -- only a minority of publishers do this. Third, the quality of the metadata varies widely between references, even from the same publisher -- Bookends will display the best information it can, which is some cases is only the DOI.
Automatically attach a PDF to a matching reference in your library:
When attaching individual PDFs, if a DOI or stable JSTOR URL is found you will have the option to "Attach to new or existing reference". If checked, Bookends will try to match the PDF to an existing reference and, if found, attach it. If there is no match in your library Bookends will download it from the Internet and then attach the PDF. This replaces the previous feature that only offered to download the reference from the Internet and then attach the PDF.
Imported references will be added to the selected static group:
If no static group is selected or more than one group is selected, the imported references will belong to the All group.
Minor update of the database engine:
Previously Bookends just examined the first selected reference for attachments.
Bug fixes:
Fixed a bug that prevented attached web archives from being displayed in the lower pane. Fixed a bug in online search that could cause an error to be thrown if data wasn't returned by the online provider. Fixed a bug that could corrupt the default reference Type options. Fixed a bug that prevented the right-click option "Add To Group" from working. Fixed a bug that prevented user-defined Term Lists from being loaded. Fixed a bug in smart folders where searches restricted to certain groups could return incorrect results. Fixed a problem that prevented some references whose metadata were obtained from CrossRef from being imported. Fixed a bug that prevented the last 10 Import Types from being included when an import filter was saved. Fixed an issue where color labels were not preserved when updating the database.
Misc:
Checking for updates when you're offline will no longer block until a timeout
Updated Google Scholar searches to deal with changes made by Google
Updated Refs -> Get DOI to deal with changes made by CrossRef
When doing an Autofill From Internet, existing keywords will be merged with newly download ones
Improved Retina image support

New in Bookends 12.8.1 (May 13, 2017)

Major update to the database engine:
This should improve performance and stability. Note that libraries created with Bookends 12.8.1 are not backward compatible. When you open a library made with an older version Bookends will make a copy and update the copy to the current version. The older library will be untouched and can still be opened by the older version of Bookends if necessary.
Modified internal database structure:
The schema simplifies storage and retrieval of of attachments and color labels. Note that any existing SQL/REGEX searches involving these properties will need to be recreated.
Set a default PDF reader in preferences:
This is useful if you are using cloud sync with Bookends for iOS. In that instance the Finder will try and fail to open any PDFs in the attachment folder in Bookends itself. You can prevent this by assigning a default PDF reader in Bookends preferences.
Removed direct import from Delicious Library:
Now you can tell the Finder to open .bib files with Bookends for import when the file is double clicked.
Reference navigation changes:
The navigation commands in the Refs menu (First, Last, etc.) now apply to the references showing in the list. Previously these commands caused the All group to be shown before navigating to the reference.
File -> Export Attachments will be enabled if any selected references has an attachment:
Previously Bookends just examined the first selected reference for attachments.
Email individual PDFs:
The option to email the PDF being viewed and the reference metadata has been added to the PDF pop-up menu. This allows you to send just the PDF you're looking at, as opposed to all the PDFs that may be attached to the selected reference, which is what the E-mail button and right-click options do.
Bug fixes:
Fixed an error that could be thrown when switching from a list sorted by color label to the single column view. Fixed an issue with some PDFs where a last page with a null label value caused an error or crash when attaching. Assigned Control-Option-Command-D to View -> All Fields to avoid a conflict with the macOS dictionary lookup shortcut. Fixed a bug that prevented Bookends from immediately offering the correct import filter for RIS, BibTeX, and EndNote Export (Refer) text files. References found on Google Books are correctly imported by drag and drop. Fixed a bug that caused some boolean online searches to either fail or throw an error. Fixed a bug in the Bibliography window in which the number of hits shown was incorrect. Fixed an issue where the OK button was always disabled when the Global Change -> Modify File Tags dialog opened even if the combobox had default text. Fixed a bug in assigning the proper text encoding when doing a drag and drop find/replace in a Term List. Fixed a bug that prevented changes made by drag and drop in a Term List from being synced. Fixed a bug in scanning Word documents where the * metacharacter was ignored for author-date citations. Fixed a bug in author-date scanning that caused the authors to be omitted form the second citation of the same reference. Fixed a bug in the format catalog that would cause the same formatted text to be output repeatedly regardless of the format name. Fixed a bug that prevented changes made to Terms by drag and drop in a Term List from being synced. Fixed a bug that prevented the Spotlight search from finding attachments whose name contained a colon. Fixed a bug where changing the subscript metacharacter didn't stick.
The temp citation metacharacters [- (replace parens with square brackets and exclude authors) and = (suppress Ibid.) work with Mellel
Get PDF From Internet works with more publishers
Removed export of references as a "Bookends 10-11.1.8"-compatible file
Bookends will only import one DOI from an online search even if it is present in multiple tags
The menu option: Refs -> First Selected scrolls to the first selected reference
The keyboard shortcut is Control-Command-S.

New in Bookends 12.8 (Mar 20, 2017)

When attaching a PDF, if Bookends finds a JSTOR stable URL on the first page it will offer to import the metadata from JSTOR
More publisher web sites are compatible with automatic downloading of PDFs
If a Type name includes the word "article" Bookends will treat the Volume fields as it does for periodical publications.
Search your library using metatags:
Search for metatags, defined in preferences, by ending the search word or phrase with an ellipsis (either 3 periods in a row or a true ellipsis, …, which is entered with Option-; on a US keyboard). For example, if you have a metatag "Colors" that contains the terms "pastel" and "primary", and "primary" has a subtag containing the terms "red" , "green", and "blue", doing a search for "Colors…" (without the quote marks) is the same as doing a search the the term "pastel" OR "primary" OR "red" OR "green" OR "blue". A search for "primary…" is the same as searching for "red" OR "green" OR "blue". You can restrict searches to a specific field (e.g. Keywords). Note that you can't mix metatag searches with normal word searches -- if the last word is terminated with an ellipsis Bookends will consider all of the words in the box to be part of the metatag name. If there is no matching metatag, a normal search using those words will be performed. You can search for metatags in Live Search, Find (Command-F), and smart groups. In the latter cases this applies to "word beginning with" and "whole word" searches–if you search for "characters" Bookends will perform a literal search for the text you entered.
Google Books online search:
Note a few peculiarities: the total number of hits found can change if you ask for more than 10 references to be returned as the search is done iteratively in batches of 10. Although the references found generally match those found when searching Google Books in a browser, the order in which they are returned may not be the same.
Command-Option-drag can now include hypertext links to multiple references at once:
How these are handled depends upon the receiving application (e.g. Tinderbox or DEVONthink Pro).
The Find dialog (Command-F) has a Reset button:
This means that Bookends will expect a volume number and an optional issue number in parentheses. Other Types treated in this fashion are "Magazine" and any Type with the word "journal" in the name.
Bug fixes:
Fixed a bug where the default folder settings in preferences were not correct if the folder was in a Dropbox folder subfolder. Fixed several issues that could affect the appearance of corporate names output with various capitalization options. Fixed a bug in live search where words containing underscores were not found. Fixed a bug in metatags where third-level subtags were not found and used in searches. Fixed a Subject Bibliography bug that could cause all references to be output when grouping by Color Label. Fixed a number of cosmetic bugs in the Online Search window. Fixed a bug where there could be an extra empty column in the reference list. Fixed a bug that allowed scanning to proceed even if no formats were enabled. Fixed a bug that prevented Bookends from importing attachments exported with an RIS file from Zotero. Fixed a bug where edits that only changed text case were not synced via the cloud. Fixed a bug in .odt scans where the style of the first character of an author's name could be incorrect. Fixed a bug that could cause a reference to receive a color label by mistake when adding it via a menu to a group with the same name as the label.

New in Bookends 12.7.9 (Feb 20, 2017)

Added = as a possible superscript metacharacter.
Newly imported references will be shown immediately when a smart group is selected and the references belong to that group.
Bookends will warn you if you try to add or edit a file tag in a locked PDF.
Bookends will remove the ? and * characters from PDF file names it generates
This is to improve interoperability with non-HFS Plus file systems.
Introducing hierarchical metatags, including keywords, in the tag cloud:
You can define metatags (previously called virtual tags) that include one or more related tags. For example, you could create a metatag "Solid Tumors" that has the terms "colon cancer", "hepatoma", and "lung cancer". If any references have one or more of these keywords, the tag "Solid Tumors…" (the ellipsis identifies this as a metatag) will appear in the Keyword tag cloud. Clicking on it will find all references with one or more of these keywords. Moreover, you can create a hierarchical relationship between metatags, much as you can with folders and groups. For instance, you might create another metatag "Hematopoietic Neoplasms" and include "lymphoma" and "leukemia". Both "Solid Tumors" and "Hematopoietic Neoplasms" could be placed under a third metatag, "Cancer". Clicking on "Cancer…" in the Keyword tag cloud would find all references in both the Solid Tumor and Hematopoietic Neoplasia metatags. Right-clicking on a metatag will display a selectable list of all its direct tags as well as daughter metatags. Hierarchical metatags work for all tag clouds except Authors and Editors. Note: metatags containing multiple words only work with the Keywords tag cloud because, by definition, the Title, Abstract, and Notes tags are individual words.
Improved PDF annotation handling in macOS 10.12 (Sierra):
This update has workarounds for a number of problems introduced in Sierra, the major one being that annotations once again have a gray highlight rectangle when selected. Highlighted text that has content (i.e. user-added information) will have a red highlight rectangle when selected.
Added a metacharacter to suppress the use of Ibid. for a particular citation:
If a temporary citation begins with =, Bookends will not output an Ibid. in the final scanned citation even if it were otherwise called for. This is handy, for example, when a citation occurs at the end of one section (e.g. a chapter) and again at the beginning of the next, and the use of Ibid. in the latter would be confusing. This feature does not yet work with Mellel.
The Find dialog (Command-F) has a Reset button:
Clicking this will set all fields to empty and pop-up menus to their factory default options, which may be useful if you are performing multiple complex searches in one session.
Bug fixes:
Fixed a bug that could cause an error when searching PubMed and finding references with issue numbers. Fixed a bug in importing BibTeX files. Fixed an error that was thrown when trying to save Google Scholar searches. Fixed a bug in scanning RTF files that could cause some temporary citations to be missed. Fixed a bug where an error message could be thrown when scrolling through the results of an Amazon search before all the references had been returned. Fixed a bug that could cause citations in unscanned/rescanned NWP documents to lose the text style of the paragraph they are in. Fixed a bug in scanning NWP documents with images where the document could be truncated. Fixed a bug in Bookends for iOS sync where the first initial of an author's name was omitted. Fixed a bug where virtual tags created with a right-click were not saved. Fixed a bug where the format Type and not the reference Type was output when the metacharacter y was used in a format. Fixed a bug where the factory default tag cloud stopwords were not installed in fresh new installs of Bookends. Fixed an importing bug that could cause the issue in the Volume field to be repeated. Fixed a bug where changes in import filter settings for parsing names weren't saved. Fixed an import bug where filters having Source parsers would cause an error. Fixed a bug that could cause a crash when syncing attachments with Bookends for iOS over Wi-Fi. Fixed a formatting bug when using surname-only in secondary citations.

New in Bookends 12.7.8 (Jan 21, 2017)

Implemented a workaround for a scanning bug in Microsoft Word 2016 15.28 and later:
The scanned document should once more retain hidden citations, text size, and document styles.
Unchecking an automated PubMed search in the Import Filters Manager clears the search history:
If the list of references previously found and ignored gets very large over time, showing the results of searches can become slow. Unchecking and checking the search again can improve performance.
Optimizations in the import filter format:
Note that import filters created or edited with Bookends 12.7.8 or later will generate an error message if used in earlier versions of Bookends.
Restored some PDF annotation features that were unavailable in Sierra due to macOS bugs:
There are still problems for which no workaround has been found, and for the time being we recommend that you avoid Sierra, especially 10.12.2 and later.
Added a Library of Congress Z39.50 import filter:
Unlike the built-in Library of Congress search, this filter will retrieve Unicode (e.g. accented) characters from the Library of Congress. To import them correctly, set the Bookends menu File -> Import Text Encoding -> UTF-8.
Bug fixes:
Fixed a bug in Google Scholar import where the wrong reference could be imported. Fixed a bug that caused an error when Bookends Server returns a formatted reference. Fixed an bug in generating a format catalog where the format couldn't be opened. Fixed a bug where an error was thrown if you opened Preferences without having an Internet connection. Fixed a bug that could cause Bookends to throw an error for some edited formats. Fixed a cosmetic bug where the entire displayed result would be highlighted after doing an advanced Google Scholar search. Fixed a bug that could on rare occasions cause the Summary view to have an orange background. Fixed some issues with converting old custom formats to the current schema. Fixed a bug in autocomplete paper where attachments could be renamed even when the "rename attachment" checkbox was unchecked. Autocomplete Paper now works when searching the Library of Congress. Prevented an error that was thrown when the Online Search window was closed before the reply was received. Fixed a bug that caused an error on opening a library when the backup prompt checkbox was checked in preferences. Fixed a bug in Wi-Fi sync with Bookends for iOS where the unique ID was not being transferred. Fixed a bug in formatting author surnames in small caps.
Styled text in abstracts and notes is shown in the Summary view
Autofill From Internet can use JSTOR if the reference has a stable JSTOR URL
Automatic PDF downloading in Bookends Browser works with Nature Communications
Updated some queries used in advanced PubMed searches to deal with changes made by PubMed
When outputting names as surname-only in small caps, small caps will be applied to institutional names (i.e., names terminated with a comma)
Obtain the full hierarchical pathnames to groups in your library via an AppleEvent
Implementation details can be found in the User Guide.
Worked around changes at Amazon so that cover art can be downloaded again

New in Bookends 12.7.7 (Dec 14, 2016)

Greatly expanded sources from which you can Autocomplete Paper:
In addition to the built-in sources for Autocomplete Paper, you can use Amazon, arXiv, the Library of Congress, and any Z39.50-compliant institution for which Bookends has an import filter. The same filters available in Online Search (i.e. checked in the Import Filter Manager) can be used when you do an Autocomplete paper.
Created workarounds for PDFKit bugs in Sierra 10.12.2 that crashed Bookends:
Note that in Sierra 10.12.2 you can’t make annotations other than highlights and may not be able to see notes and comments in the Bookends PDF annotation view. Until Apple fixes these bugs or we can work around them, avoid upgrading to Sierra 10.12.2.
Improvements in Bookends Browser:
Reference detection in web pages is more robust, automatic downloading of PDFs works with more journals, and web pages are loaded much more quickly. To avoid long delays in parsing web pages with many DOIs, Bookends will limit the DOI candidates it detects to 30.
You can combine the [ and - metacharacters in a temporary citation:
This will remove the author name from the final citation and have parentheses converted to brackets. Use like this: {[-temp cite}. This feature does not yet work with Mellel.
The hit (marked) status of a reference will be retained in the daughter when you Replicate as Book Chapter:
This means that if you are showing the Hits list when you perform this function, the new (replicated) reference will appear without you having to show All.
Bug fixes:
Fixed a bug with two different source parsers that imported from sequential tags in a text file. Fixed a bug in the pdf annotation view where the Command-+ and Command-- keyboard shortcuts for zoom in and zoom out didn't work. Fixed a bug that prevented removal of format Types that the user tried to delete. Fixed a bug in a descending sort of the single column list when Date Added or Date Modified was in use. Fixed a cosmetic bug in automated PubMed search were the line showing author names could be duplicated. Fixed a bug where the tag cloud stopwords were ignored if the user modified the default setting. Fixed a bug that caused Mellel to remain in the front when some scans were initiated. Fixed a bug that could cause an error to be thrown for some automated PubMed searches. Fixed a bug in proofreading scans where a backslash before and after literal text would be doubled. Fixed a bug where the pop-up menu that selects what type of files to show in the Open File dialog could be disabled by mistake. Fixed a bug in the generation of BibTeX keys where incorrect or illegal text could be included if the first author's name was not entered as surname, first name. Fixed a bug in Autofill From Internet where chapters could have the book title and chapter title mingled in the Volume field and the DOI of the chapter was replaced by that of the book. Fixed an error that occurred when emailing a non-PDF attachment when "remove annotations before sending" was checked in preferences. Updated the PubMed parser so that author affiliations are imported again.
Updated the automated PubMed search to work around changes made by NCBI
The setting for automatically renaming a PDF when Autocomplete Paper is remembered between launches
Import books from PubMed
Bookends will treat .nbib files exported from PubMed as text files when you try to import the references
Bookends will automatically escape "type" to "[type]" if necessary when an SQL search is entered and saved by the user
Remove Duplicates based on DOI or PMID
Improved identification of certain publication titles when importing from CrossRef
The order of annotations shown in the note stream better corresponds to the order in the PDF

New in Bookends 12.7.6 (Oct 5, 2016)

New in Bookends 12.7.5 (Sep 12, 2016)

In the Manual Remove Duplicates sheet you can unmark all references with the right-click hierarchical menu item "Unmark All"
A notification is generated when wifi sync with Bookends On Tap is finished
Updated PubMed access to use the NCBI HTTPS servers
Added user-configurable limits of 100 and 500 MB to the size of PDFs that can be synced with Bookends On Tap
Bookends will display the contents of attached text files with the extension .tex or .ris
Open PDF attachments in PDF Expert
When specifying a default custom folder location in preferences, Bookends will not create a "Bookends" subfolder if you have named the parent folder "Bookends"
Improved detection of reference metadata found on Google Scholar
Autocomplete Paper can now be invoked by a right-click option on a reference with an attachment
When you do a live Spotlight search, the search phrase will be highlighted in yellow if found in the PDFs associated with the found references
Two new citation delimiters: [[ ]] and >:
These may be useful for those using LaTeX or writing math-intensive papers in which the other citation delimiter options conflict.
Modified filters will be copied, not moved, to the Custom Import Filters Folder:
This means that if you want to revert from an edited version of a filter to the version we distribute, all you need to do is delete the format in the Import Filters Manager (select it in the Import Filters Manager and press the Delete key) and the original filter will be shown. Filters that are in the Custom Import Filters Folder are shown in bold.
The reference list will not redraw when clicking on empty space in the groups pane:
This well avoid lengthy redraws when working with very large libraries.
Bug fixes:
Fixed a bug where Bookends failed to use the author and title word "ignore list" when sorting bibliographies. Fixed a bug in Autocomplete Paper that prevented some searches from working with Google Scholar. Fixed a rare bug that could cause Bookends to throw an exception when displaying a newspaper article. Fixed a bug that could cause a problem when scanning with formats that use Ibid. Fixed an error that could happen when setting the custom folders location in preferences to Default. Fixed a bug in Proofreading Scan for Word and Nisus Writer Pro. Fixed several bugs in proofreading scans of text files. Fixed an importing bug where some field tags ending in a colon would not be recognized. Fixed a bug where the attachment display in the editable reference pane did not refresh properly when there were multiple attachments of text or Mellel files. Fixed a bug that could cause an error when opening preferences. Fixed a bug where the first letter of the second half of a hyphenated first name was dropped when converting to initials. Fixed a bug in importing Source fields where the field tag and the metadata are on separate lines. Selecting an import filter that cannot be verified as such now generates a warning rather than an error. Fixed a bug in scanning Word documents where the bibliography font was not set to the default.

New in Bookends 12.7.4 (Aug 8, 2016)

E-mailing references with attachments works with Microsoft Outlook 365
Updated importing of unicode characters from Google Scholar to deal with changes made by Google
Search within the results of an online search:
When performing an online search, Bookends will import the results into a temporary database. Press Command-F to reveal a live search field that lets you search among these references. Any text in the lower pane of the search window that matches your search will be highlighted in blue (as opposed to the orange highlighting of text that matches the online search field). You can search all reference fields or selected fields (click on the search field pop-up triangle to select among these). Note that the corresponding import filter determines which metadata are imported, and you can edit the filter if you want information other than the default to be imported (e.g. to import MESH headings to Keywords in the PubMed filter). The search field pop-up triangle also lets you select previous searches, which are remembered when you press Return while the cursor is in the search field.
Search history is remembered in the main library window:
The popup menu in the library window live search field will remember previous searches so that they can easily be performed again. Note that it doesn't record all of the partial word searches that may occur as you type. To have the search remembered, you must explicitly press Return while the cursor is in the live search field.
Include hypertext links in reference fields:
You can paste hypertext links to references in Bookends itself (created with Edit -> Copy HyperText Link -> Copy As Link) or in other applications (e.g. DEVONthink Pro) into any fields in the Main tab or the Notes field in the reference edit pane. These links are live, and clicking on them will take you to the corresponding record. This will not work with reference fields in the Additional Fields tab, and if you edit a notecard containing a hypertext link the link will be converted to plain text. Note that only Paste will insert a live hypertext link, not Paste And Match Style. So if you have assigned Command-V to the latter, you must use Shift-Option-Command-V to use the keyboard to paste in a hypertext link.
Autocomplete Paper will indicate references that you already have in yellow:
The criteria used to determine if an online reference is the same as one in your library will be a matching DOI, PMID, or URL, depending on the online source.
The minimum allowable height of the library window reference list has been reduced:
This means, for example, that the viewing area of the bottom pane is greater if you invoke Maximize PDF Display when viewing PDF attachments.
Bug fixes:
Fixed a bug in OpenURL that prevented users from accessing any but the first URL entered. Fixed a bug where a beep sounded when doing a type-ahead search in the Online Search window. Fixed a bug that could cause an error to be thrown when filling out a reference of Type newspaper. Fixed two bugs in formatting citations citations, one that prevented the name in a subsequent citation from appearing as specified, the other that caused incorrect placement of et al. Fixed a bug in Mellel scans that resulted in incorrect output when using cited pages followed by ad hoc text. Fixed a bug in author-date citations where the italics setting for et al. was ignored. Fixed a bug in Google Scholar import where the Type could be mistakenly set to Artwork. Fixed several bugs in importing from JSTOR and other filters that parsed a Source line. Fixed a bug in scanning where every letter in a temporary citation was considered to be a separate citation. Fixed a bug that prevented Autocomplete Paper from working with Web Of Science. Fixed a bug in Autocomplete Paper from PubMed where entering certain characters would cause a malformed URL error. Fixed an error that could be thrown when shift-selecting more than one author/editor in the tag cloud display.

New in Bookends 12.7.3 (Jul 15, 2016)

New file structure for preferences:
The new preference file, called Bookends Preferences and stored in the ~/Library/Application Support/Bookends folder, is much smaller than the old, will not grow in size over time, and is resistant to corruption. Existing preferences as far back as Bookends version 11.0 will be converted to the new schema automatically. If you are upgrading from Bookends 10.x or earlier, preference settings will be reset to the defaults.
Find a group:
Use the Action pop-up menu under the groups pane or click on the group list header to search for a specific group. If a match is found Bookends will select that group and scroll to it. If you type in only a partial name, Bookends will search for a group that begins with those letters and select the first one it finds. You can't search for the three mandatory groups: All, Hits, and Attachments.
Improved single column reference list
Bookends remembers the field the list is sorted by when you click on the column header to toggle between descending and ascending sorts. Cosmetic changes.
Improved drag visual feedback:
The textual content in the drag of items in the reference list will be displayed (e.g. either the temporary citation or, if the Option key is held down, the formatted reference). The pdf proxy icon will be displayed when it is dragged. Previously, only the rectangular outlines of these items were displayed.
Improvements to OpenURL:
Bookends now supports arguments that specify the DOI or PMID: rft_id=info:doi/ and rft_id=info:pmid/, respectively.
Bug fixes:
Fixed a bug in Autofill From Internet that uses the ISBN where an editor's name was missed. Fixed a bug where some in-text citations could be missed when scanning a NWP document that as pictures. Fixed several bugs in formatting that affected sorting and numbering of references in a bibliography. Fixed a bug that prevented an online search from being performed if you selected the terms from the search history pop-up menu while the search button was disabled. Fixed an issue that caused an error to be thrown when scanning with certain formats. Fixed a bug that could cause an error when loading preferences. Fixed a bug in the default field settings for the Newspaper Type. Fixed a bug that could cause edited format settings to be saved to the wrong Type if the Type pop-up was used before the information had been saved.

New in Bookends 12.7.2 (Jun 19, 2016)

New in Bookends 12.7.1 (May 22, 2016)

Improvements to Database Maintenance -> Rebuild and Repair:
If these operations are successful, the original library will be moved to the Trash with a date and time stamp added to its name. The newly rebuilt or repaired copy will be given the name of the original, making the entire process transparent to you. If there are problems, the original file will be left where it is and you'll find the rebuilt or repaired version in the same folder.
Integration with Manuscripts:
Manuscripts (http://www.manuscriptsapp.com) is a word processor that handles its own formatting of references and bibliographies. If Manuscripts is selected as your linked word processor, Copy Citation will send the reference information in a form that Manuscripts can convert to its internal citation scheme. In addition, Manuscripts can now request reference metadata from Bookends (please see Manuscripts documentation for details). These features require Manuscripts v1.1.3.
Improved AppleEvent support:
If you use an AppleScript to retrieve formatted references (the GUID event), you can ask that the references be returned as EndNote XML instead of in a formatted form. In this case a request to return the information as RTF will be ignored.
Online Search has been upgraded to use the HTML/1.1 protocol
The boolean setting (AND/OR) for how to combine search results when multiple are selected is remembered between launches
Bookends can use a DOI in any field to find the reference online:
If you have one or more DOIs in any field in the edit pane (e.g. Keywords, Notes, the DOI field, etc.), right-clicking on that field will bring up a list of the DOIs that you open in your browser. Each DOI must be on its own line.
Improved single column reference list:
The field used to sort the list is shown in the list header. You can now sort by Rating.
Italics in book titles will toggle to plain text if the format calls for the field to be italicized
The extension .ris will be added to a file exported as plain text using the RIS format
Improved detection of keywords when importing from PubMed via Online Search
Bug fixes:
Fixed an issue where a Rebuilt synced library would perform an unnecessary cloud sync when it was closed.
Fixed a problem where a DOI in a PDF could be mistakenly found on PubMed and the wrong metadata imported.
Fixed a spurious error that could occur when checking for a new version.
Fixed a bug that could cause an error when syncing with Bookends On Tap.
Fixed an error message that could appear after doing an autocomplete paper using Web of Science.
Fixed multiple issues with Bookends Server.
Fixed an issue where reference sync status was included when copying a reference from one library to another.
Fixed a bug where Autofill From Internet could increment the disambiguating letter in the Key field if BibTeX was enabled.
The date modified will not be changed when dragging a reference from one library to another.
Fixed a bug that could cause an error when using Global Change -> Modify PDF Tags.
Fixed a bug that in rare cases could cause a spurious number to be added to a citation date during disambiguation when formatting.
Fixed an issue where importing many references from the watch folder using a slow Internet connection could have unpredictable consequences.
Fixed a bug where drags from a Term List were not being displayed in the reference field.
Fixed several bugs dealing with formatting metatypes.
Super- and subscripts will render properly when sending a bibliography to disk as styled text.

New in Bookends 12.7 (Apr 25, 2016)

Improved DOI detection in PDFs
Importing from Google Scholar will work when you have set the language in Google Scholar to Turkish
If TeX markup is enabled, smart open and close apostrophes will be converted to ` and ', respectively
When using Bookends Browser, Command-] and Command-[ will move forward and back, respectively
Improved retrieval of conference proceeding metadata from CrossRef
Bookends will use an en dash rather than a hyphen in a citation group with a sequential range of reference numbers
Global Change -> Modify PDF Tags has an updated UI
Bookends will ignore images in notes when importing references from Sente XML
Made changes to the Bookends Browser JSTOR parser to deal with changes made by JSTOR
Detection of accented capital letters for services such as small caps is much improved
Drag a browser's PubMed reference link onto a static group to import to that group
If you use a custom reference Type whose name contains the characters "[Book]" or "[book]", Bookends will enable the Refs -> Replicate As Book Chapter menu item
Sync reference libraries via the cloud:
Bookends uses iCloud Drive—all you need is your Apple ID and password to log in, then you don’t need to think about it again. Refer to the User Guide (Help menu) for instructions on setting up cloud sync. Cloud sync requires OS X 10.10 (Yosemite) or later.
Sync new or edited formats, import filters, and journal glossaries in the cloud:
Bookends creates “custom” folders for newly created or edited formats, import filters, and journal glossaries. Their default locations are in your user Library: ~/Library/Application Support/Bookends/. You can cloud-sync these files between computers by moving them to the folder created by a cloud storage and backup service such as DropBox, Google Drive, Microsoft OneDrive, etc. On each computer where you use Bookends, go to Bookends preferences (General tab) and tell Bookends where these sync-service folders are on the local drive. In that folder Bookends will create a new folder called Bookends (if it doesn't already exist) and place the custom folders in it. Bookends will use that folder to save or access any custom files. Note that you must allow read/write permissions to the shared folder or you will get an error when Bookends tries to save to it.
The old mechanism for syncing Bookends databases has been removed:
If you are using a pre-Yosemite version of OS X, you can sync libraries via a file-sync service like iCloud Drive, Dropbox, Google Drive, Microsoft OneDrive, etc.
Refactored DOI detection in Bookends Browser:
In addition to DOI detection being faster and more accurate, metadata will be imported from PubMed when possible.
Display author first names as initials in the reference list:
This option is set in preferences (Lists tab).
Italicized words in a title will toggle to plain text if the format calls for an italicized title:
For example, if your format outputs titles in italics and there is an italicized species name in a title, that name will be output in plain text and the rest of the title in italics.
The arXiv id will be imported into User1:
If you are using this field for the BibTeX key, in the arXiv import filter position the tag "arXiv:" in front of another field to hold this id.
Updated Google Scholar search to deal with changes made by Google:
Imported references will once again represent the best metadata Google Scholar has.
Modified formats will be copied, not moved, to the Custom Formats Folder:
This means that if you want to revert from an edited version of a format to the version we distribute, all you need to do is delete the format in the Formats Manager (select it in the Formats Manager and press the Delete key) and the original format will be shown. Formats that are in the Custom Formats Folder are shown in bold.
If an attachment or library is on an external volume such as a server, Bookends will not attempt to mount the volume if it's not already available:
Trying to mount an unavailable volume can result in an apparent hang.
Improvements in the generation of BibTeX keys:
If you have told Bookends to warn you if a key is not unique and also have asked Bookends to create keys when importing, Bookends will simply create the keys when importing without asking for every non-unique key field. If you have more than 26 references with the same base key (author + year) Bookends will use as many lowercase letters in the key as are necessary to disambiguate them. The key field will be disambiguated if necessary when duplicating a reference.
Limit the length of the file names Bookends suggests for attachments:
Limit the length of file names suggested for attachments by Bookends. This is useful if you have Bookends automatically rename attachments. This value is set in preferences (General tab) and the range is 20–200 characters (excluding the extension).
Added smart quotes for Polish:
Set in preferences (Scan & Bib tab).
Citation identifiers in Sente XML files will be imported into the User20 field:
This will make it possible for you to scan documents that have temporary citations inserted by Sente.
The update notification dialog is much more informative:
This will be used to notify you of future updates.
Remove a PDF Finder tag associated with a library:
This allows you to remove incorrect tags (e.g. typos) and tags you no longer use.
Bug fixes:
Fixed a bug that could in some cases cause a crash when manually removing duplicates. Fixed a bug that could cause a crash when importing a tag beginning with an asterisk. Fixed a bug in drawing the Term List pushpin on Retina displays. Fixed a bug that prevented Refs -> Insert Date from working in the Additional Fields tab. Fixed a bug in Autocomplete Paper using Google Scholar where some search characters could cause the search to hang. Fixed a bug in which the Type column in the reference list where there are multiple selected lines was not updated immediately after a global change. Fixed a bug where some characters could be output as UTF-8 even though BibTeX conversion of Unicode to TeX was enabled. Fixed a bug where the "Generate a bibliography" checkbox could be disabled when doing a Mellel scan. Fixed a bug that could cause an error to be thrown when importing an existing bibliography using CrossRef. Fixed a problem where the Word 2016 AppleScripts were not installed when the user's machine didn't have an Application Scripts folder. Fixed a bug that could cause a hang when importing some MARC records. Fixed a bug in searching notecards for character strings enclosed quote marks. Fixed a cosmetic bug in File -> Go To URL where the online search window controls might not be rendered properly. Fixed a bug that prevented windows from being moved to the top of the screen when System Preferences -> General -> Automatically hide and show the menu bar was checked. Fixed an issue with RIS imports where the starting and ending pages numbers could be reversed.

New in Bookends 12.6.5 (Jan 31, 2016)

New in Bookends 12.6.4 (Jan 2, 2016)

New in Bookends 12.6.3 (Dec 7, 2015)

New in Bookends 12.6.2 (Nov 16, 2015)

Smart folders (nested smart groups and more): A smart folder is actually a smart group that can contain other groups and folders. If a smart folder has no content, clicking on it is the same as clicking on a smart group. However, if you have placed other groups inside it, when you click on the smart folder all the searches it contains will be executed. The result will be an AND or and OR of all the searches, depending on your setting in the Action pop-up menu beneath the groups pane (also accessible with a right-click in the Groups pane). This is powerful feature that lets you nest searches. And if you open the smart group by clicking on its disclosure triangle, you can click on any of the groups or folders it contains to perform just that subset of searches. Note that smart folders, just like normal folders, do not sync with Bookends On Tap.
Make Quoted Highlight From Selection: This option, available in the PDF Action pop-up menu in the lower display pane, will highlight the selected text and add metadata to it: the page (e.g. @5) and the text as a quote (i.e. preceded by a >), which will be displayed in a notecard. Press Return or Enter immediately after performing this command to add to or edit the notecard. Be aware that the contents are stored in the PDF, not the Bookends database, and so can have multiple consecutive Returns. This replaces the older option "Make Quoted Note From Selection".
If you select a PDF highlight or note and the note stream is visible, Bookends will select the corresponding notecard
Set default PDF highlight color: Set this value in the PDF Action pop-up menu, or by right-clicking on the color indicator in the PDF toolbar.
Malformed URLs will be ignored when importing XML
Improved import of DOIs from BibTeX text files
If you omit "http://" in a Bookends Browser URL, Bookends will add it when doing a search
Right-click on a picture attachment to zoom in or out
Bug fixes:
Fixed a bug in the notecard Find in PDF function that could prevent quoted text from being found.
Fixed several problems with the display of picture attachments in the standalone reference window.

New in Bookends 12.6.1 (Oct 24, 2015)

Improved ability of Bookends to find a DOI in an attached PDF
Many enhancements in the handling and display of PDF annotations in the note stream
(1) If a line in a notecard begins with >, Bookends will consider it to be quoted and display it as indented text in gray to indicate that fact. (2) New menu option: Make Quoted PDF Note From Selection. When you select text in a PDF, this option will create a new note (in the PDF) and begin each line with > to indicate that it is quoted text. You can add comments on the line immediately following the last line of quoted text. (3) New menu option: Highlight Selected Text and Make Bookends Notecard. This will highlight the selected text and import it into Bookends as a quote. The corresponding notecard will include the page (e.g. @23). Press Enter immediately after this if you want to add comments to the notecard. (4) When adding a PDF annotation or a notecard, Bookends will automatically scroll to in the note stream. (5) Find notecard in PDF will use quoted text, if any, for the search. This means that if a line begins with >, indicating quoted text, that will be used for the search. If one doesn't exist, the first line of text (excluding a header) will be used.
New scripts for Word 2016:
These scripts will be automatically installed if you have Word 2016 installed on your Mac, and will appear in the Add-ins tab in the Word ribbon. If for some reason they are not installed you can do that manually, the scripts and instructions being available in ~/Library/Application Support/Bookends/Scripts for MS Word. Note: these scripts are a temporary solution. Microsoft is developing a new mechanism for adding third party add-ins to the ribbon, and when it is available we'll transition to it.
Improved importing of Sente XML:
If you have quotes in Sente notes, they will be converted to Bookends quotes when imported (e.g. a > will be placed in front of each line).
Improved display of headers in notecards:
For notecards that contain both a header and text, the header will take up only a quarter of the display, leaving more room for the text.
When a library is opened, Bookends will select the reference that was showing when it was last closed:
Returns interfere with Google Scholar searches.
Bug fixes:
Worked around a bug in El Capitan to restore Show In Finder. Fixed a bug in Mellel scans where before and after quoted text in a citation was ignored. Fixed a bug in scanning a Mellel document where consecutive reference numbers weren't converted to a range if italicized numbers were being output (e.g. Science format). Fixed an problem that could occur when parsing an EndNote XML file yielding an "The path passed into new FolderItem was invalid" error. Fixed a bug in Mellel scanning where Ibid could be incorrectly used when a citation matched the last citation of a preceding group.

New in Bookends 12.6.0 (Oct 4, 2015)

File -> Import References From EndNote:
EndNote must running with an open database. The options are to import All references or just the Selected references. Any EndNote attachments will be moved to a subfolder in the Bookends default attachment folder called "EndNote Attachments" (the EndNote file/folder organization will not be preserved). You can import references from EndNote into a Bookends group by selecting that group in the Bookends library window before initiating the import. Note that if a PDF with the same name is already in the Bookends folder called "EndNote Attachments", the EndNote PDF not be moved and the existing PDF will be considered the attachment.
New UI for comparing duplicates and references:
This applies to the side-by-side comparisons you see with Refs -> Remove Duplicates -> Preview and Verify and with Refs -> Compare References. Clicking on the ❖ symbol in front of a field will bring up a control containing that field from both references. You can quickly copy the field from one reference to the other with arrowhead buttons, or you can copy/paste only selected text from one to the other. Changes are not committed until you click the Save button (or you can click Close to exit without changes). Command-clicking on the ❖ symbol immediately moves that field's contents to the corresponding field in the other reference, no other clicks are required, and this is undo-able.
After a notecard search, Bookends will switch to the note stream view in the right pane if it is not already selected
New option to generate BibTeX citekeys as lowercase only:
This setting is in the BibTeX tab in preferences.
Bookends now works with Mellel Lite:
Mellel Lite must be specified as the default word processor in preferences for full functionality.
Return characters will be automatically removed from searches done in Autocomplete Paper:
Returns interfere with Google Scholar searches.
If CrossRef returns malformed XML when attaching a PDF, Bookends will alert you to this and attach the PDF to an empty reference
Updated PubMed import function to deal with changes made by PubMed:
This corrects a problem where the reference Type was set to Artwork.
Updated Bookends Browser detection of JSTOR reference information to deal with changes made by JSTOR:
Note that because of the variability in the way different reference types can be displayed, Bookends cannot detect and/or import all references.
Improvements in the way that Bookends detects PDF highlights for display as notecards
Output the text representation of a reference's color label in a formatted reference
Use the & symbol in the format's Order field.
Bug fixes:
Fixed a bug where Hits menu options were disabled after doing a Refs -> Remove Duplicates and choosing to put the duplicates in the Hits List.
Fixed a problem where dropping a reference from the Online Search window onto the library window to import would result in a hang.
Fixed a formatting bug where using ^^ to tell Bookends what to output if there are two or more editors gave incorrect results.
Fixed a bug where attaching a file to multiple references at once failed if the file was copied or moved to the default attachments folder.
Fixed a bug in Title Case where a letter after a smart apostrophe or en dash was always converted to lower case.
Fixed a bug in Pages scanning that could cause a hang for certain footnote citations.
Fixed a bug in the Mellel scan where arbitrary punctuation that came after cited pages (e.g. @p\,\} was repeated.
Fixed a bug in Concise View where clicking on a link to another reference took you to the wrong reference.
Fixed several display issues in the Concise View where some text was mistakenly underlined.
Fixed an issue with Google Scholar that prevented some references from being identified if there was only one match and Google Scholar thinks may not be correct.
Fixed a problem in Bookends Sync where sync wasn't being offered on database open even if that option was checked in the Sync Configure window. Fixed a bug where Bookends would not recognize .gloss (journal glossary) files created in another application.
Fixed a bug in scanning where the option to have no punctuation before and a closing parenthesis after a citation was ignored.
Fixed a bug that caused a return to be output in citations where multiple references are grouped under one number.

New in Bookends 12.5.9 (Aug 23, 2015)

File -> Import References From Sente - Sente must running with an open database. This command will switch from Bookends to Sente where you select the references you want to import (Command-A selects all). When finished, either press Command-Y or click the Select button in the dialog Sente puts up. You will switch back to Bookends and the references will be imported. Any Sente attachments will be moved to a subfolder in the Bookends default attachment folder called "Sente Attachments" (the Sente file/folder organization will not be preserved). You can import an individual collection from Sente into a Bookends group by selecting that group in the Bookends library window before initiating the import.
Improved Remove Duplicates -> Preview & Verify Duplicates - (1) Red arrowheads will appear in front of fields that differ between duplicate references. Clicking on an arrowhead will move the field from one reference to the other, allowing you to extract the information from a reference before it is deleted. (2) In the lower reference display pane, the reference that will be saved will always appear on the left and the one to be removed on the right.
Improvements in emailing references and attachments - You can now send attachments via Microsoft Outlook if that is your default email client (set in Apple Mail preferences).
The Bibliography Window UI has been updated - Superscripts and subscripts are now rendered, hanging indents are shown, and you can use a toolbar and ruler to adjust the bibliography.
The formatted view pane displays superscripts and subscripts
Double-click a tag word to create new tag cloud based upon the references displayed
This is much faster than using the corresponding menu to drill down through your references to find useful related tags.
Static group names are sorted in the smart group definition window
DOIs that are part of a URL will be extracted and imported if the import filter has a corresponding tag
The Compare References window is now read-only, it doesn't support copying of text from one reference to another
Improved detection of DOIs in PDFs from Science
Attach a file to more than one reference at a time - When using drag and drop or Refs -> Attach File, the file will be added to all selected references, not just the first selected reference. This may be useful, for example, if you have a PDF of entire journal and want to add it to each individual article in that issue.
Bug fixes:
Fixed a bug where a file tag search would fail if the path to the default attachment folder had been changed in preferences.
Fixed a bug the prevented importing of pdfs from Bookends Browser when you right-clicked on the PDF proxy icon.
Fixed a bug in setting the bibliography output style in preferences.
Fixed a bug where the value of the "PDFs only" checkbox was was not set correctly in the watch folder configure window.
Fixed a bug in Remove Duplicates where the reference list did not scroll when using the arrow keys or the buttons to change the selection.
Fixed a problem in BibTeX imports where an internal quote mark could cause an imported field to be truncated.
Fixed a problem in Yosemite where Bookends couldn't determine the default email client.

New in Bookends 12.5.8 (Aug 3, 2015)

Show the groups a reference belongs to in the reference list display - You can add a column called Groups in preferences (Lists tab) or by right-clicking on a column. Bookends will show all static groups that each reference belongs to, separated by commas.
When selecting a folder in the groups pane, Bookends will honor the boolean AND/OR setting for virtual groups when displaying the folder's contents - This means that you can tell Bookends to display any reference in any group in that folder, or just the references that are in all of the groups in that folder. The pop-up menu "Virtual Groups" was changed to "Multiple Selections" to better reflect its function.
Improvements in extracting notes from notecards - When right-clicking on a notecard, Copy Notecard or Copy Notecard With Citation will copy just the styled text of the note to the clipboard, ignoring any headers, cited pages, or tags. The latter will not automatically switch and paste into a linked Mellel document, but will do so with all other word processors.
Improved downloading with Bookends Browser - The UI has been simplified, so that if only one library is open an import button is shown, otherwise a pop-up menu is available that allows you to select the library to import into. A "download PDF" checkbox tells Bookends whether to try to import the PDF or not.
Add a reference to a group in the All Concise View - Click on the label "Groups" and create a new group for the reference or select from the existing groups.
Remove Duplicates has the option to "Put Duplicates in Hits List" - This will make hits of all replicates and display them in the library window reference list.
Bug fixes:
Fixed a bug that could cause SQL errors to be thrown if a folder containing certain smart group combinations was selected.
Fixed a bug in the direct Google Scholar search that caused a single hit to be ignored.
Fixed a bug in "Flatten Group Hierarchy" that could cause folders to retain false information about their contents.
Fixed a problem using the watch folder where when the default attachment folder was on a different volume.
Fixed a bug in applying Refs -> Replicate as Book Chapter to a reference of Type Book Chapter.
Fixed a problem where rare DOIs were not imported with Online Search.
Fixed a bug in Sente XML export where an attachment name could be imported twice.
Fixed an error that could be thrown during a Sente XML import if the author had a first name but no surname.
Fixed a bug that would sometimes cause a message to be shown when opening the standalone reference window.
Fixed a bug in Global Change -> Change Field where a leading return character in the text to be added could be ignored.
Fixed a bug where outputting complete last pages in a format was applied to Roman numerals (it is now restricted to Arabic numbers).
Fixed a bug where straight apostrophes typed into SQL searches were converted by the system to smart apostrophes, causing SQL errors to be thrown.
Fixed several issues with Autofill from Amazon.

New in Bookends 12.5.7 (Jul 3, 2015)

Improved importing of reference metadata and attachments exported from Sente as Sente XML
Include final citation in formatted bibliography reference - If you enter the + (plus) symbol in the Bibliography Options order field, Bookends will replace it with the citation that was inserted for that reference during a scan. The enclosing punctuation (e.g. parentheses) are not included. This works for author-date and custom but not numbered citations. If the + is entered in the Citation Options order field it will be ignored.
Spotlight used from within Bookends will search webarchives
Updated the PMID -> PMCID converter - Bookends uses the latest and very fast NCBI APIs, which are much better at finding PMCIDs than the older versions.
If available, the PubMed Central ID (PMCID) will be imported from PubMed searches
Updated importing of JSTOR metadata when using Bookends Browser to deal with changes made by JSTOR
Go To URL will show the URL of each selected reference in your default browser
Previously, only the URL of the first selected reference was shown.
The menu Generate BibTeX Key is enabled even when BibTeX is not enabled in preferences
This means you can now create a "citekey" in the User1 field for your own purposes.
Bug fixes:
Fixed a bug in scanning where using ^ in an author-date format beginning with the letters "APA " did not cause " and " to be used instead of " & ".
Fixed a bug in scanning Pages where enclosing punctuation (e.g. parentheses) around an italicized number were also italicized (i.e. the Science format).
Fixed a bug in scanning where an author-date citation in which the name was supposed to be italicized came through as marked up plain text.
Fixed a bug when scanning with the Science format where consecutive references weren't being consolidated into a range.
Fixed a bug in automated PubMed search where previously found references were not ignored in subsequent searches.
Fixed an error that was thrown when drag-reordering searches in an import filter.
Fixed a bug where the URL for Web Of Science was outdated.
Fixed a bug where text enclosed in backslashes in cited pages did not replace the text specified in the format for "after cited pages".
Fixed a bug that moved the folder containing an .odt document to the Trash if you aborted a scan of that file.
Fixed a bug where the break binding character in a format could cause the preceding field to be output twice.
Fixed a bug in scanning .odt files where the punctuation separating citations in a group could sometimes be omitted.

New in Bookends 12.5.6 (Jun 8, 2015)

Unchecking "Automatically Resize" in the PDF annotation view display the PDF at its the actual size
This setting is remembered between launches and will be used when the same or a new PDF is displayed (the setting is used for the PDF display pane in the lower part of the library window and the Attachment tab in the edit reference pane/window). If you want to toggle between the actual and the resized display without setting that as the default, right-click on the PDF and select "Automatically Resize" or "Actual Size" from the hierarchical menu.
You can choose to open PDFs with the application Highlights - If you click on the metadata of a PDF in the application HIghlights, Bookends will come to the front and show the corresponding reference in Bookends
If the reference is not found in the Bookends library, the link to the reference will be opened in Bookends Browser, where you can read and/or import the reference. Note that Highlights and Bookends use DOIs to identify references, so if it is missing (in Bookends) or not registered by CrossRef these functions won't work.
Export PDFs without annotations - The Action pop-up menu in the PDF annotation view lets you export the PDF being displayed with annotations (i.e., "as is") or without annotations. When using the latter, Bookends will remove all markup: notes, comments, highlights, and line drawings (circles, squares, etc.).
Email PDFs without annotations - If this option is set in preferences (Internet tab), when emailing a reference with a PDF Bookends will make a copy of the PDF in the Trash and send that link to Appe Mail. The duplicated PDF will be deleted when you next empty the Trash. The original PDF attachment will not be touched.
When emailing a single reference, Bookends will tell the email client to use the article's title as the Subject
Bug fixes:
Fixed a bug in importing unicode characters from a Google Scholar search.
Fixed a bug in Copy Citation with Scrivener where the temporary citation wasn't being automatically inserted.
Fixed a bug where a reference could be formatted incorrectly if there was no format Type corresponding to the reference Type.
Fixed a bug in Spotlight OR searches.
Fixed a problrm where Copy Citation or Copy Formatted didn't paste into the linked Scrivener application.
Fixed a bug where super/subscripted metacharacters were not being resolved in the bibliography when scanning a Pages document.
Fixed problems in the note stream when copying cited pages in notecards with a header and tags.
Fixed a bug in parsing author names when importing a BibTeX file.
When scanning a document with an author-date format and asking for the authors to be placed before the citation with the ^ metacharacter, an " and " will be subsituted for an " & " if the format name begins with "APA" (this previously worked with custom, but not author-date, citations).

New in Bookends 12.5.5 (May 18, 2015)

Improvements in the ability and speed of Bookends to resolve DOIs
Improved Watch Folder that can be used by multiple users - The watch folder behavior has changed in several important ways. It now registers each addition of a file to the watch folder, rather than repeated examining the watch folder for the presence of files. A new option in the watch folder Configure dialog is to move or copy files to the default attachments folder. If you tell Bookends to copy files, the original will be left in the watch folder. This makes it possible for more than one person in a group to watch the same folder (e.g. on a server), providing an easy mechanism to distribute the same PDF and references to many people. Note that this also means that when you "start watching", any files already in the watch folder will be left alone -- you would have to drag them out and then back in for Bookends to register their addition and then move or copy them to the default folder.
Add multiple PDF tags at once - You can add more than one tag at a time by clicking in the Tag field (PDF annotation view toolbar) and pasting a Return-delimited list of tags. Note that this will not work when editing an existing tag.
Importing from Google Scholar will work when you have set the language (in Google Scholar) to something other than English - Supported language settings are: Arabic, Catalan, Chinese, Croatian, Danish, Dutch, English, French, German, Hebrew, Italian, Japanese, Portuguese, Spanish, and Serbian.
Enhancements to the manual remove duplicates window - The window is now a sheet instead of modal dialog, and the unique ID of each reference is displayed.
Add references and attachments to a library via an AppleScript - This feature will be used by an upcoming release of DevonThink Pro. See the User Guide for the syntax if you want to use it with your own scripts.
New import filter file format - Import filters created in or edited by Bookends 12.5.5 cannot be used by earlier versions of Bookends.
Bug fixes:
Fixed a bug that caused an error to be thrown when viewing a reference with multiple attachments in the editable reference window and selecting an item in the attachment pop-up menu.
Fixed a bug that prevented entry or editing of tags in the reference edit pane/window.
Fixed a bug in locating PubMed references with the Bookends Browser data detector.
Fixed a bug in importing using a PDF doi that was found on PubMed.
Shift-Command-O now opens the PDF showing in the standalone reference window Attachments tab.
Fixed a cosmetic bug that prevented the top of the window the directly abut the bottom of the menu bar.
Window -> Term LIst menu options are now enabled when the standalone reference window is in front.
Fixed a bug introduced in 12.5.4 where autofill from internet could fail for references found on PubMed.
Fixed a bug in scanning where styled numbers in citations were incorrectly applied if there was preceding literal text.
Fixed a bug where on rare occasions the name order for "others" did not correspond to the format setting.
Fixed a bug in importing an internet reference Type from Bookends browser where the URL could be incorrect.
Fixed a bug that under some conditions could result in data entered into a new reference to be added to an existing reference.
Fixed a bug where scanning of text files could cause a hang.
Fixed a bug where the unscan dialog was not closed after scanning a document.

New in Bookends 12.5.4 (Apr 6, 2015)

Integrated PDF tags:
If you are running OS X 10.9 (Mavericks) or later, tags will appear in the toolbar in the annotated PDF view. Click on the field labeled Tags to enter a new tag manually, or right-click to choose from a list of tags already defined in the Finder or in the database (you can use the keyboard or the arrow keys to quickly locate the tag you want in the list). Click on a tag name to bring up a pop-up menu that lets you edit or remove it from the PDF. Any of these operations can be applied to all selected references as well. Refs -> Global Change -> Modify PDF tags is another way to Add or Remove tags from the selected references, the Hits List, or the entire database. If attachments are displayed in the Summary view (set in Preferences), any tags will be shown in parentheses after the attachment names.
Consolidate attachments:
This Global Change option will move attachments that are outside of the default folder to the default folder or a subfolder you select. Attachments already in default attachment subfolders will not be moved. This operation can be applied to the selected references, the references in the Hits List, or to all the references in the library.
PubMed improvements:
Bookends will import accented (Unicode) characters, and you can import full first names (rather than initials) by using the FAU tag in the import filter.
Greatly decreased the time needed to save very large note streams
Bookends will ensure that new database file names end with the extension ".bdb"
Added \citenum as a recognizable citation delimiter for BibTeX scans
Updated parser for importing existing bibliographies to deal with changes made by CrossRef
Bug fixes:
Fixed a bug in Autocomplete Paper when using the standalone editable window.
Fixed an error message in Sente XML import that could occur if some expected metadata wasn't there.
Fixed a bug where specifying a Type other than default when creating a new reference wasn't honored.
Fixed a bug that would cause an error to be thrown if you generated a subject bibliography based on groups twice in a row.
Fixed a bug in scanning where the last digit of a cited page could be omitted if the ^ metacharacter was used in the temp citation.
Fixed a bug in the concise view where attachments could be shown twice instead of links.
Fixed a bug where "Rename PDF" didn't work in the standadlone editing window.
Fixed a bug where the sort preference for the one column view was not always used.

New in Bookends 12.5.3 (Mar 9, 2015)

Display or hide the Notes field in the main tab of the reference edit pane/window - This setting in preferences (Refs tab) tells Bookends whether or not to display the Notes field on the main tab (there is already a separate tab devoted to Notes). If you elect to hide it, the Abstract field becomes twice as large and will expand more rapidly when the window height exeeds that necessary to display all fields. Hiding the Notes field is a good option for those with small screens who want to maximize the amount of text they can see in the main tab without scrolling.
Add attachments when using the standalone reference window - Use Refs -> Attach -> File or Folder.
Better migration of references from Sente to Bookends - When exporting from Sente, Sente XML files contain more information than EndNote XML (for example Sente XML includes notes, comments, and the date the reference was added). This information can now be imported into Bookends, the notes and comments becoming notecards.
Changes to navigation in the reference list - The Refs menu navigation commands (First, Next, etc.) now apply to the order of the references in the list (previously the intgernal order of the reference in the database was used). This is a much more natural way to use these commands to move through the list. The Hits navigation menu items have been removed because they are redundant.
Combine cited pages and a header in the same notecard - This is an example: #@12 This is a header. The # tells Bookends this is a header, the @12 (which must end with a space or a return) is the cited page.
When editing a notecard, pressing Enter will close the field and save the changes
Bug fixes:
Fixed a bug where text style could be missing in the Summary pane when using a format to create the display.
Fixed a bug where the editable reference window wasn't updated properly when replicating a book as a book chapter.
Fixed a bug in scanning citations in author-date format where the author was placed in front and cited pages were used.
Fixed a bug where the default reference font was not used in the standalone reference editing window.
Fixed a bug that could cause Bookends to miss citations in NWP documents with many images.
Fixed a bug where text in an active edit field was lost if the user moved to another reference via the Refs menu.
Fixed a bug that could cause a scan to hang on rare occasions.
Fixed two bugs with New Ref and the editable reference window where either it didn't open or it opened with the contents of another reference showing.
Fixed a bug where the ! metacharacter in a temp citation was ignored during a scan.
Fixed a bug in Global Find and Replace where an error could be thrown when operating on a single field.
Fixed a bug where EZProxy settings were ignored by Bookends Browser if you entered the URL manually.

New in Bookends 12.5.2 (Feb 23, 2015)

New in Bookends 12.5.1 (Feb 17, 2015)

New in Bookends 12.5 (Feb 9, 2015)

New icons for the application and library files, and an updated user interface - Removed: (1) the standalone reference window, (2) setting font, font size, and colors for the note stream, concise views, and the Term List pane in the main library window.
Merge or replace multiple Terms at once - To merge Terms, drag and drop one or more items in a Term List onto another and Bookends will offer to merge them (i.e. replace them with the one that received the drop). To replace Terms with new rather than existing text, select all the Terms you want to change, right-click on the Term List, and select “Replace…” from the hierarchical menu.
Show live linked references in the concise view - You can have Bookends display a list of references the selected reference is linked to (e.g. a book linked to a book chapter) in the concise view pane on the right. The unique ID of the linked references will be shown and act as hypertext links that take you directly to the linked reference.
Open any browser web page or PDF in Bookends Browser - Sonny Software provides a bookmarklet, labeled “Open In Bookends”, that you can install in your browser’s bookmark bar by drag-and-drop. If the page has references that Bookends can import, or contains a PDF you want to import, click on “Open In Bookends” and the same web page/pdf will be automatically opened in Bookends Browser. You can install the bookmarklet from this web page.
The functions that scan Word and RTF files and for handle groups have been entirely rewritten - These changes will allows us to more easily deal with bugs and add features going forward.
Omit names from final citation is improved - Using - in front of a temp citation results in removal of the author and editor names in the final citation. If the reference is a Book Chapter, only the authors’ names will be removed.
Pressing Escape while editing a notecard or the concise view no longer closes the edit field and discards edits - To ensure data aren’t lost inadvertently, only clicking the Cancel button will do that.
If you close the library but leave Bookends running, Bookends will open that library again automatically if you click on its icon in the dock
The Import Filter Manager and Journal Glossary windows now have a File -> Save menu (Command-S)
References found with a search of Google Scholar that have DOIs matching references in your library will be highlighted in yellow
This may be useful when outputting reference metadata in formats such as RIS or EndNote (Refer) that are intended for import into other reference managers. The symbol is m, and multiple attachments will be separated by returns.
The list of saved searches in the Online Search window can be sorted by name or date of last search by clicking on the corresponding column header
The full title will not be substituted for an empty short title in a conditional group
This means that if a conditional group is {s}, nothing will be output if the short title is empty. If you want the full title output in such a conditional group, you'd use this: {s^t}.
Add URL to bookmarks - Whenever you are using Bookends Browser, you can bookmark the current URL by clicking on the bookmark icon and selecting Add URL As Bookmark.
Updated JSTOR online search and the search in Bookends Browser to deal with many changes made by JSTOR
Updated Google Scholar search and autocomplete to deal with changes made by Google
On launch, Bookends won't automatically open a library that was moved to the Trash
If Bookends has to use CrossRef to validate DOIs, Bookends Browser will show up to 10 references found by the DOI data detector on a single page
This is to prevent excessive waits for verification by CrossRef when there are many dozens of DOIs on a page.
Bug fixes
Performing a proofreading scan on a text file containing BibTeX-style temporary citations is no longer allowed.
The - metacharacter in temporary citations now works with .odt author-date scans.
Fixed a rare bug where literal text in a temporary citation could be repeated in a subsequent citation.
Fixed a bug that could cause a crash when adding a PDF highlight annotation to the note stream.
Fixed a bug where the PDF popup menu had the options for note stream display were available when it was invoked in the reference edit window Attachment pane.
Fixed a bug where newly highlighted text was not added immediately to the note stream.
Pressing tab when editing a notecard saves any changes before closing the field being edited.
Fixed a bug where rich text in a field would lose the style information when edited in the Concise View.
Fixed a bug that could cause a crash when updating a term list for an empty library. Fixed a crash that could occur when the import text encoding was set to UTF-8 and an invalid character was found.
Fixed a bug in obtaining DOIs from CrossRef that could slow down or prevent retrieval of PDFs from some sites using Bookends Browser.
Fixed a bug in which edits in an enlarged Notes field were not immediately updated in the Notes tab.
The View -> Attachment option is now correctly checked when the selected reference has no attachment.
Fixed a bug that could cause the number before a bibliography reference to be output in bold if the authors were bolded.
Fixed a bug in which the tag cloud pop-up menu text was not updated when a group changed.
Fixed a bug that could truncate the document when doing an author-date scan with year-only after multiple cites by the same author enabled.
Fixed a rare bug that could cause autocompletion of heavily used terms to fail.
Fixed a bug where an incorrect DOI would be returned from a PDF that does not contain a DOI.

New in Bookends 12.2.4 (Nov 18, 2014)

A more appropriate error message will be shown if you use the watch folder to import more than 50 references when running in demo mode
You can’t annotate or markup a locked PDF in the annotated pdf viewer
A small lock icon will appear in the PDF display toolbar to tell you that the PDF is locked. In this case you cannot add a note, comment, highlight, or underline to the PDF. You can make an unlocked copy of the PDF in Preview or Acrobat and attach that if you want an editable copy.
Updated Bookends Browser to deal with changes made by ScienceDirect and the American Chemical Society
Updated CrossRef parser so that titles that contain colons will be imported in their entirety
Removed keyboard shortcut for Fonts -> Show Colors It conflicted with the shortcut for Autocomplete Paper.
Improved the identification of PDF highlighted text for display in the note stream
If a temp citation consists of only literal text (e.g. is between backslashes), that text will be output in the final citation as if it were a reference
Note that you will get unpredictable results if this is used with a format that outputs numbers rather than text for final citations.
Duplicate references without attachments - This option in the Refs menu lets you make a duplicate reference that is identical to the original except that it will not have any attachments.
The relative widths of the Abstract and Keywords (or Notes) field in the editable reference pane are remembered between launches
Output attachment full path names in a formatted reference - This may be useful when outputting reference metadata in formats such as RIS or EndNote (Refer) that are intended for import into other reference managers. The symbol is m, and multiple attachments will be separated by returns.
Modified the CrossRef importer to correctly deal with DOIs and URLs - This was broken because of changes made by CrossRef.
Bug fixes:
Fixed a bug that could cause text to be output in tiny sizes when metatypes were used.
Fixed a crash that could occur when importing and attaching a PDF based on its DOI.
Fixed a problem where right-clicking to remove styles from a reference field would cause the text to be deleted if had not first been automatically saved.
Fixed a bug in the Online Search window where the Search button could be mistakenly disabled.
Fixed a case where an error would be thrown if a word whose case was not to be changed contained an open but not a closed bracket.
Fixed a bug where two open parentheses were output for citations by number where there was quoted text between backslashes at the beginning of the temporary citation.
Fixed a bug in scanning .odt files where the * metacharacter in a temp citation resulted in the output of only the year for Author-Date formats.
Fixed an error message that could be thrown if an attachment has an illegal file name.
Fixed a bug that interfered with the setting of ratings with a click if they were in the first column of the reference list.
Fixed a bug that caused an error to be thrown if you imported a PDF to an empty reference when a static group was selected in the library window.
Fixed a bug in the hierarchical menu that appeared when you right-clicked on a URL field that had more than one URL.
The paper clip attachment icons now appear correctly on Retina displays. EndNote XML references for web pages are now correctly imported as type Internet.

New in Bookends 12.2.3 (Sep 15, 2014)

Open an attached graphic in the program that created it by double clicking on it in the library window
Improved citation handing - If a citation ends with a period and a quote mark, the period will be suppressed for all citations in a group except the last..
Improved speed when saving notecards edited in the note stream
Bug fixes:
Fixed several bugs in which an error could be thrown when manipulating an annotated pdf in the standalone reference window.
Fixed an error that could be thrown when performing a Bookends Sync.
Fixed a bug in metatypes where a return was not placed after a metatype reference output in the bibliography.
Fixed a bug where an editor name might not be placed in front of a citation even if the ^ metacharacter was used.
Fixed a cosmetic issue with misalignment of the reference list in the library window.
The option to import references exported from Bookends to the Hits List option works again.
Fixed a bug where the attachment tab wasn't updated correctly in some circumstances.
A period following the cited pages after an Ibid. will be suppressed for all citations in a group except the last.
Fixed a bug in Global Change where the ¬ character was not being converted to a Return.
Bookends will no longer try to download pdfs of books from JSTOR via the direct search (they are not supported by JSTOR).
Fixed a bug that could distort the UI when resizing the library window and require a force-quit.
Fixed an error in drag and drop of a pdf onto a group folder and attaching the pdf to a new reference.
Fixed a bug in adding a new reference when Hits was selected in the group pane.
Subject bibliographies work again (broken in 12.2).
Fixed a bug that could cause bibliographies to be output in hit order instead of sorted in some cases.
Fixed a bug where an extra empty notecard was added when adding a notecard to the note stream.
The list of reference Types shown in the library window will be updated instantly if it is edited in preferences.
Fixed a bug in Option-Shift where smart groups that were not supposed to find references in static groups were highlighted in yellow by mistake.

New in Bookends 12.2.2 (Jul 30, 2014)

New in Bookends 12.2.1 (Jul 14, 2014)

Show highlighted PDF text in notecards:
If this option is turned on in the pdf view Action popup menu, any text highlighted in the PDF will be shown as a virtual notecard when the note stream is visible.
The notecard will be the same color as the highlighted text, and a small lock icon at the upper left indicates that it cannot be edited. If the highlighted text has an associated note, the text of each (the highlighted text and the note) will be shown in its own notecard.
If you select a notecard representing highlighted text and press the Delete key, the highlight will be removed from the PDF.
Show PDF note modification dates in the note stream:
This option can be toggled on/off in the pdf view Action popup menu.
Maximize/Minimize PDF Pane:
Expands or diminishes the height of the PDF display pane in the library window. Available via the PDF Action popup-up menu and keyboard shortcuts.
Updated the Google Scholar parsing to deal with changes made by Google
Name suffixes (e.g. Jr.) will be omitted when the secondary order is used to create a custom citation.
Bug fixes:
Fixed a rare bug that could cause two reference imported from PubMed to be placed into the same record.
Setting fields User5 through User20 with an AppleScript no longer generates an error.
Fixed a bug that could cause an error to be thrown when adding a new reference.
Fixed a bug is Cited Pages that resulted in failure to move a preceding comma before a closing quote mark.
Fixed a bug that could cause an error to be thrown when editing a reference and then clicking on the Inspector button.
The library window can no longer be dragged when in full screen view.
Fixed a bug in scanning a text file where a numbered final citation could include the author's name.
Fixed a bug that could cause an error to be thrown when right-clicking in the Attachment tab to detach a pdf that couldn't be found. The paper clip attachment images now update properly when moving the library window between a non-retina and a retina display.
Fixed a bug in printing the selected references.

New in Bookends 12.2 (May 26, 2014)

New PDF viewer with search, markup, and annotation:
The new PDF rendering engine has the following features:
(1) search for words and phrases in the pdf,
(2) thumbnail page view,
(3) markup PDF text with highlighting and underlining,
(4) create and edit PDF notes and comments,
(5) create a note associated with highlighted text, and
(6) position and reposition notes and comments on the PDF page. Any markups or annotations that you create in Bookends will be visible in any applications that uses PDF Kit (e.g Preview and Adobe Acrobat). To use the new PDF viewer in the library window, select “Use Annotation View for PDFs” in the Action pop-up menu underneath the reference list.
Tight integration between PDF notes and the Bookends note stream - When using the PDF annotation view, PDF notes will automatically appear as virtual notecards at the end of the note stream (highlighted in a color different from reference notes, which is configurable in preferences). Clicking on a virtual notecard will instantly take you to the note in the PDF. Any edits you make in the PDF note will appear in the corresponding virtual notecard, and any edits you make in the virtual notecard will be written back to the PDF. Text selected in the PDF can be imported into Bookends as a permanent and searchable notecard. You can also right-click on any notecard and search for its text in the PDF.
Move groups between folders with a hierarchical menu - Select one or more groups (static or smart) in the groups pane and right click. You will have the option to move the groups to an existing folder or to a newly-created folder. If anything other than a static or smart group is selected this option will not appear.
Watch folders work when the default attachment folder is not on the boot HD
Use AppleScripts to set the contents of a field
Bibliography generation is faster
Set text output style (e.g. Styled Text, BibTeX, HTML, etc.) in Preferences, Scan & Bib tab
This can also be done in Biblio -> Bibliography.
Worked around a Mendeley XML incompatibility with EndNote XML so that reference Types are imported correctly
The keyboard shortcut for Autofill From Internet has been changed to Shift-Command-A
If Bookends can't find an assigned attachment folder, the factory default folder will be used
JSTOR search and Autocomplete Paper were updated to deal with changes made by JSTOR
The number of references you can import from Google Scholar at once has been reduced from 50 to 20
This is to prevent Google Scholar from thinking that you are a web bot and banning your i.p. address.
Updated Google Scholar parsing to deal with changes made by Google
Existing font styles will be preserved when pasting decomposed Unicode text into a text field
Smarter handling of Title Case
Bookends will not capitalize a letter if it occurs immediately after a number or a period.
New menu item Refs -> DOI -> Copy DOI
Bug fixes:
Fixed a bug in the Import Filter Manager that prevented the hierarchical menu option Show Filter in Finder from working.
Fixed several small bugs dealing with using "\cite" with BibTeX citations.
Fixed a number of bottlenecks that caused delays when formatting fields with many text styles.
Fixed a bug that could cause the first reference returned in a Google Scholar search to be skipped.
Fixed a bug that could cause references already found by an automated PubMed search to be displayed in subsequent automated searches.
Fixed a bug where the space between the author and date would be omitted when using the ^ to place the author in front of unenclosed Author-Date citations.
Fixed a bug that caused the key field and the reference Type to be ignored when importing a BibTeX file.
Fixed a bug that caused the wrong reference to be edited when creating a new reference with a smart group selected.
Fixed a bug where using a right-click to add a reference to a group could result in the wrong group being modified. Worked around a bug in the framework that could cause an exception to be thrown when formatting styled text.
Fixed a bug in setting proxy information in preferences.
Fixed some mis-mappings of accented characters in BibTeX output.
Accented characters are now really replaced by their ASCII counterparts when the BibTeX Key field is generated.
Fixed a bug where a trailing comma in the title could be included in the formatted output.

New in Bookends 12.1.2 (Apr 5, 2014)

New in Bookends 12.1.1 (Mar 3, 2014)

Bookends will find many more pdf attachments for references in EndNote XML files exported from Sente
Title words beginning one or two spaces after a semicolon or period will be capitalized when Title Case is used, even if they're on the exclude list
Previously, only words beginning one space after the semicolon or period were capitalized.
Library of Congress and Google Scholar searches were updated to work around changes made by those services
If a format calls for the last two digits of the second page in a page range be output, a leading 0 will be ignored
The right-click contextual menu in the group pane has an option to rename the selected group
Bug fixes:
Fixed a bug that could cause mangled reference metadata to appear in the reference list.
Fixed a bug where editing the Notes field on the main tab would not update the Notes field in the Notes tab.
Fixed a bug that could cause an error to be thrown if you edited a tag while the tag cloud was showing and then clicked on the tag cloud.
Fixed a scanning bug that prevented the year from being output when a citation used the year-only modifier (%) and had cited pages.
Fixed a bug where the font size of scanned in-text citations would be different from that of the paragraph's style sheet.
Fixed a bug in excluding words from capitalization where words consisting of a single accented character were ignored.
Fixed several bugs in case conversion that affected Title Case and Sentence case.
Fixed a bug that resulted in malformed citations if you scanned a Word document twice in the same session with an Author-Date format.
Rating stars in the list view can no longer appear as white on a white background in refs that have been assigned a color label.
Fixed a bug in Find in This Reference.
Fixed a problem that prevented dropped text onto a note stream from being added to the new notecard.
Cited Pages once again work in scanned text files.
Bookends Server works once again.
Fixed a problem where a Find/Replace with styles could change the style for an entire field.
Fixed an issue with JSTOR where the search would have to be done a second time for it to succeed. Corrected the escaped BibTeX output for é.
Importing metadata from Web of Science in Bookends Browser works again.
The Key field, if shown in the reference list, will update automatically if you use Refs -> Generate BibTeX Key.
Fixed a bug where an author's surname was always used if a secondary order field in the format had content, even if the popup told Bookends to use the same name format as the first time.

New in Bookends 12.1 (Jan 6, 2014)

Bookends 12.1 requires OS X 10.7 (Lion) or later:
This is necessary because OS X 10.6 (Snow Leopard) is no longer supported by our development tools. Databases created with Bookends 12.1 and later (until the database schema changes at some time in the future version), however, are still compatible with Bookends versions 12.0 through 12.0.7.
Attachment Flow:
Like Apple’s Cover Flow, this view will present a carousel showing the first page of all files attached to the selected references. Move to the attachment (usually a pdf) that you want and press Return, click Select, or double click on it to have that reference selected with the attachment shown in the lower pane. Press Escape or click Cancel to exit the Flow view. Attachment Flow is presented in a movable modal window with the same dimensions as the library window to make reading the contents easier.
Drag and drop creation of a static group in a specific folder:
A folder in the groups list will highlight if you drag one or more references over it. When you drop, Bookends will offer to create a new group that will be placed in the folder. If you drop on any line that is not a folder or a static group, Bookends will add the new group outside of any folder.
Spring-loaded group folders:
If you drag references and hover over a closed folder for a second, the folder will flash and then expand to reveal its contents. If you hold the Option key down while hovering, all subfolders will expand as well. The folders will not automatically collapse if you move the cursor away without making a drop.
Improved automatic installation of a format or import filter:
If you double click on a format or filter, or drop one on an open Bookends library, and the format or filter already exists in the corresponding Custom folder, Bookends will offer to replace an existing format or filter of the same name, keep both, or cancel the operation. Previously, the format or filter already existed, it would automatically keep both. If there is no existing format or filter of the same name in the Custom folder, the new item will simply be moved there.
OpenURL 1.0 compatibility:
If you enter "url_ver=Z39.88-2004&" (without the quote marks) in the Search Arguments (Preferences, Metadata tab) Bookends will understand that the query should be OpenURL 1.0-compliant. Bookends will then add the prefix "rtf." before any field name when the query is sent (you should not enter that in the query string yourself, Bookends will do that for you).
The "Bibliography Formatter" menu item has been renamed "Bibliography"
Bug fixes:
Fixed a bug that prevented certain Chinese and Korean characters from being output in citations or bibliographies when styled text is applied.
Fixed a bug in the Import Filter Manager that prevented Bookends from finding a filter selected in the list pane.
Fixed a bug where the Preferences password field for an authorized proxy server was invisible.
Fixed some BibTeX accented character escape sequences.
Smart groups can once again be used for Subject Bibliographies.

New in Bookends 12.0.7 (Nov 25, 2013)

UI update completed:
Major changes in preferences, minor tweaks elsewhere.
Scan Pages 5 documents:
Bookends is unable to directly scan saved Apple Pages 5 documents, which have an undocumented file format, no APIs, and limited AppleScript support.
However, if you have a document open in Pages 5, you can use Biblio -> Scan Open Apple Pages Document to scan it.
The scanned document will be saved in Pages '09 format, which Pages 5 will automatically open and convert to its native format.
Note that the bibliography will not be automatically added to the scanned document, but will be in the clipboard.
After the scan, scroll to where you want the bibliography to appear (usually at the end) and press Command-V (Edit -> Paste).
Improved small cap handling in bibliographies:
When small caps are used in bibliographies, Bookends will output them to your word processor in sizes relative to the style sheet font size settings, as is already the case for citations. This works with Word, Nisus Writer Pro, and Mellel (version 3.2.7 or later).
Placing a comma at the end of the Date field will cause Bookends to output it without parsing
Bug fixes and improvements:
Fixed a cosmetic bug where the left edge of a color label was too far to the right when showing attachment icons was turned off in preferences.
Fixed a bug that prevented cited pages in an author-date citation from being displayed in Nisus Writer Pro.
Fixed a bug that caused bibliographies to be omitted from scanned RTF files.
Autocomplete works again when editing a field with a term list in the concise view.
Fixed a number of bugs that interfered with metatypes.
Fixed a bug in small caps where the last initial of a name might be output as a small cap instead of a true cap if the surname was output first.
Fixed a bug that prevented small caps from being displayed in scanned citations if cited pages were used.
Fixed a bug in hanging indents in scanned Nisus Writer Pro bibliographies.
Pasting a bibliography copied from the Bibliography Window into a word processor document will once again appear with a hanging indent if specified in the format.
Fixed a bug that could cause unwanted punctuation to be output before “et al.” when a reference was cited more than once. Fixed a cosmetic bug where color of a notecard being edited would revert to white if the library window lost and then regained the focus.
All Greek letters are now correctly converted to their capitalized form when displayed in small CAPS or ALL CAPS. Fixed a rare problem with syncing pdfs with accented characters in their names with Bookends On Tap.

New in Bookends 12.0.6 (Nov 4, 2013)

Updated user interface
Includes changes to the library, online search, standalone reference, and Inspector windows.
Updated the Google Scholar parser to deal with changes made by Google
New formatting option: surname in small caps
Improved small cap handling in Word and Nisus Writer Pro citations
When small caps are used in citations, Bookends will output them not in absolute point numbers but in relation to the style sheet font size settings.
Rename Attachments has been added to the library window right-click menu and Action pop-up
This option is available when the first reference selected has attachments, and will apply to all selected references that have attachments. To rename just the attachment you are viewing in the display pane, use the Action pop-up menu or a right click on the attachment (if Use WebKit to display pdfs is unchecked) and choose "Rename Attachment…"). You can also rename attachments in bulk with Refs -> Global Change -> Rename Attachments.
When using an APA format, if the editors name is the first item output its surname/first name order will be that set for authors
This only applies to APA formats, which Bookends detects by the presence of the 3 letters “APA” at the beginning of the format name.
The h-index option in Online Search has been removed
Turn off automatic check for updates on launch
This option, which is on by default, can be turned off in preferences, General tab. If Bookends was purchased from the Mac App Store this option is disabled because Apple has its own update notification system.
Curly brackets will be removed from fields imported with the BibTeX filter
This requires that you check Convert from TeX in the BibTeX tab in preferences.
A Google Scholar advanced search will be noted as such in the Online Search window
The color palette for reference labels has been updated
Completely new installations of Bookends will show these colors. If you are an existing Bookends users, you can install this new color palette by clicking Set To Default button under the color display in preferences (Lists tab).
Display the contents of attached TaskPaper documents in the display pane and the Attachment Inspector
Removed support for Microsoft Word 2004 and X add-ins
If you need to use these old versions of Word, write to Sonny Software and request the corresponding add-ins and/or templates.
Bug fixes and improvements
The attachment icon in the reference list is now displayed properly on Retina-enabled machines and when sorting by a column with numeric entries, such as Ref #. Fixed a bug in journal glossaries where short journal names were not being output when called for. Fixed a bug that prevented periods in journal names from being removed if the journal name was not in an enabled glossary. Fixed a bug where repeated citations with a secondary order could have "et al." output twice. Fixed a bug where cited pages would be output in italic if the preceding text were italic in Word and Nisus Writer Pro scans. Fixed a bug where scanned footnotes would use the bibliography default size. Fixed a problem where using a watch folder would result in very high CPU activity. When the insertion point is in the live search field, clicking on a reference will immediately give the list the focus. Fixed a rare bug where a translator's name could be output as dashes if the author's name was. Fixed an error message that could be thrown when clicking on a group folder that contained a smart group returning no hits. Fixed a bug when outputting formats in plain text where metacharacters in quoted text (e.g. ++ and ^^) were ignored and they were output as is. Bibliographies in Nisus Writer Pro documents once again use the default bibliography font. Fixed a bug in scanning that prevented hanging indents to be automatically added for Nisus Writer Pro and Pages documents. Fixed a bug in bibliography sorts by first author and then date. Fixed a number of bugs with metatypes. BibteX fields beginning with protected characters (in curly brackets) will not be truncated. Fixed a bug in scanning Nisus Writer Pro documents that contain pictures. Fixed a bug in scanning Word and NWP where unicode characters would be mangled in unmatched citations. Fixed several issues concerning the use of “Idem” when scanning. Cited pages once again work with Author-Date citations. Fixed a bug that prevented the library window Action pop-up menu Copy Text To…hierarchical menu from working when text was selected in the browser. Fixed a bug in Bookends On Tap sync where multiple keywords would considered as a single keyword. Fixed an error that occurred when adding or removing a virtual tag with a right-click. Fixed a bug that prevented a right-click on the pdf proxy icon in Bookends browser from importing the pdf or web archive being viewed. Fixed a bug that prevented cited pages from being added to "ibid." citations.

New in Bookends 12.0.5 (Sep 30, 2013)

Updated user interface
Bookends will import attachments from the watch folder even when it is in the background
A new option to include or remove page ranges in footnotes that use Cited Pages - The default behavior is to remove a specified page range when Cited Pages are present. Set this option in the Cited Pages section of the format.
If a format calls for the short title and that field is empty, the full title will be substituted
Empty lines created by doing a Find/Replace in the Authors, Editors, and Keywords fields will be automatically removed
A new menu item and keyboard shortcut for enter/exit full screen - View -> Enter Full Screen (Control-Command-F). This menu item will not appear if you’re running Bookends on Snow Leopard, which doesn’t support the full screen view.
Hits -> Prev/Next shortcuts have been changed to [ ] (so Option-Command-F switches focus to Live Search again)
If a journal glossary is enabled it will be used for the Book Series Title field as well as the Journal field - If the glossary entry matches, it will be used as entered in the glossary. If no match is found, the usual title capitalization rules set in the format will be used.
If Cited Pages contain non-numeric characters other than a space, dash, or en dash, Bookends will not try to adjust an ending page number as specified in the format - This means that nonstandard or complex cited pages will be output as entered.
The text font for any converted order in a pre-12.x format that has styled text will be set to Arial - This is important because in Cocoa only fonts that have italic and bold faces will show these variations (e.g. avoid fonts like Geneva and Lucida Grande). The font in the order field is not used when creating a formatted reference, but the face (bold, italic, and/or underlined) is.
Bug fixes and improvements:
Fixed a bug that would cause APA citations to always use just the first name plus et al. the second time a reference was cited.
Fixed the enlarged field view so that it is the same text style but 2 points larger than the normal field.
Fixed a bug with the watch folder feature where Bookends would have very high CPU use when in the background.
Fixed a bug that could cause an error to be thrown when a watch folder pdf was damaged.
Fixed a bug that caused an error with watch folders when renaming the pdf according to a format.
Fixed a bug that would cause an error to be displayed if you changed the reference in the standalone reference window with a right-click.
Fixed a bug that could cause an attached pdf downloaded with the library browser to contain two periods in the name.
Fixed a bug that could cause an error when entering large amounts of text in the Notes field.
Fixed a bug that could cause Bookends to output an author or author/title for a citation even when directed not to and the field had styled text.
Fixed a bug that caused an error when removing styled text from a field with a right-click in the standalone reference window.
Fixed a bug that could cause an error to be thrown when styled text data was incomplete.
Fixed a problem where styled text saved in a format's notes field would appear as naked RTF when the format was next opened.
Fixed bugs in scanning with metatypes. When generating initials from an authort’s name, accented capital letters will be included.
Superscripted characters in scanned citations will appear properly.
Fixed a bug that caused cited pages to be output twice when an en dash was used between the starting and ending page number.
Fixed a bug that prevented Bookends from creating a correct reference when using “Replicate as Book Chapter” in the standalone reference window.
Fixed a formatting bug where Bookends would obey the setting for "last author at end" even when "use et al." was unchecked.
Fixed a bug that could cause a return character to be inserted in a veriified Mellel citation that was preceeded by a metacharacter.
Fixed a situation where an error could be thrown when clicking on a folder in the groups pane.
Fixed incorrect application of smart quotes that appeared before or after other punctuation marks.
The library window pane settings are now saved when you quit Bookends without closing the window first.
Fixed a bug in APA 7th where only the first and last authors were output if there were more than six.
Fixed a problem with generating large bibliographies during a Nisus Writer Pro scan.
Fixed a bug in which a trailing period in a series titles was stripped out when formatting.
Fixed a error that could be thrown if you closed the library window while doing a PubMed search.

New in Bookends 12.0.4 (Sep 5, 2013)

New in Bookends 12.0.3 (Aug 5, 2013)

Introducing watch folders:
 When a new file is detected in a watch folder, Bookends will attach it to a new empty reference and, if a file is a pdf and Bookends can locate a doi for it, import the metadata from online sources. The file will be moved to the default attachments folder and renamed according to the specifications in preferences. If the metadata cannot be found, the title of the new reference will contain the name of the original file, prior to renaming. Watch folder settings apply to individual libraries, so different libraries can watch different folders. Settings are managed in File -> Import From Watch Folder -> Configure. You must tell Bookends what folder to watch, whether Bookends should watch for just PDFs, and if any imported attachments should be added to a particular group. Once a valid folder has been specified, Bookends will begin watching. You can stop (or restart) watching with File -> Import From Watch Folder -> Stop/Start Watching. Bookends will temporarily suspend watching when it is not the active application or the library window is moved to the background, and will resume when brought to the front. Note that if a file in the watched folder can't be moved (e.g. you don't have read/write privileges), Bookends will stop watching, as it will if the watch folder is renamed, moved, or deleted. To avoid distracting updates to the UI while you are working, newly added references will not be displayed until the list is refreshed naturally (for example, by clicking the group All). An exception is that if you are importing to a group and that group is selected, the reference list will be updated in real time. 
 Improved online metadata detection when attaching a pdf:
 When you drop a pdf on a library window, Bookends first looks for a doi in the pdf. If none is found, Bookends will search PubMed for a reference that matches the initial text of the pdf. If a single match is found, Bookends will retrieve the doi from PubMed. This allows Bookends to find more references online. One example would be a preprint of a paper submitted to a journal that was accepted (and is now on PubMed), but the pdf you have doesn't contain the doi. 
 
Greatly speeded up opening and saving the enlarged field view for fields with styled text and the standalone Notes field 
 For APA formats, an & will be replaced with "and" when author names are placed in front using the ^ metacharacter and there are 2-5 authors 
 New option for Cited Pages:
 In the Cited Pages portion of a format, you can tell Bookends to "Move leading punctuation inside of a preceding quote". This means that if a cited page is separated from the rest of the citation with a comma or a period and the preceding text ends with a single or double quote mark, the punctuation in front of the cited pages will be moved inside the quote: "The Example," p. 14. If unchecked, the same citation might look like this: "The Example.", p. 14. The former (the default) is standard for American English, the latter for British English. 
 Select references that have orphaned attachments 
 If a specific field is selected in Live Search, its name will be displayed underneath 
 Updated formats for American Society of Microbiology journals 
 When disambiguating citations by title, if quotes are called for Bookends will use the form of smart quote selected in preferences. If none is selected, English will be used. This is primarily used by the MLA format. 
 Navigation through the hits is available in the library window:
 These functions are available in the Hits menu. Note that the order of the hits is arbitrary (e.g., it might be the order of citations in a scanned document), usually not the same order as the sorted reference list. 
 The keyboard shortcut for Hits -> Next has been changed to Command-Option-F:
 This avoids a conflict with the OS X Universal Access Zoom shortcut. 
 
Bug fixes and improvements:
 Fixed a bug that could cause problems with fields with returns and styled text when converting a database to Bookends 12.
The author settings in a format's second order are honored again. Editors names will not be replaced with --- if the format calls for the authors names to be replaced in consecutive works by the same authors and editors, unless the reference is an Edited Book.
Fixed a bug that could cause references to be sorted in the bibliography even when not called for when scanning a Mellel or Nisus Write Pro document.
Fixed a bug that prevented citation disambiguation by author initials, names, or short title from working.
Fixed a bug with journal glossaries where the full name was not substituted for the short name when the short name was not found.
Fixed a bug that would cause the standalone reference window to appear when using Hits -> Go To Hit # when the library window was in front.
Fixed a problem where reference copied to the clipboard with Copy Formatted could not be pasted into some applications.
Notecard headers now appear in the correct color.

New in Bookends 12.0.2 (Jul 22, 2013)

Spotlight searches for exact matches can be performed by surrounding the search text with quote marks
If you drop a pdf on a static group, the group will be selected
You can batch import pdfs into a static group by dropping them onto the group name
The pdf image in the Attachment Inspector can no longer be dragged and dropped
The Inspector window is now a floating palette
The results of an advanced PubMed search will be labeled as such in the Online Search window
If a specific field is selected in Live Search, its name will be displayed underneath
Correct APA formatting for two authors in front of a citation:
When scanning with an APA format, if there are two authors in a citation and they are to be placed in front, " and " instead of " & " will be used to separate them.
This occurs when the temp citation begins with the ^ metacharacter and the name of the format begins with the letters APA.
Bug fixes and improvements:
Fixed a bug that could cause unwanted styles to be applied to punctuation in a formatted reference.
Fixed a bug that could insert repeated cited pages in a scanned Mellel citation.
Fixed a Word and NWP scanning bug that would cause Bookends to think two citations were back-to-back and combine them if the intervening text had no spaces and was entirely in Unicode.
Fixed a highlight that wouldn't go away after dropping a pdf on a static group.
Database Maintenance operations now work on libraries that have an ampersand (&) in their names.
Fixed a bug that caused a delay when double-clicking on a pdf in the Attachment inspector.
Fixed a bug that would cause all but the last reference in a bibliography grouping (i.e.
under one number) to lose styled text.
Fixed a bug that would cause the authors to be formatted incorrectly in a bibliography after dashes were used to replace repeated authors.
A comma at the end of a title once again means that no special casing will be applied to that title.
The bibliography for a scanned text file is now properly placed in the clipboard.
Fixed a bug that caused Global Change -> Change Field to malfunction.
Fixed a bug that caused text entered in the Concise View to sometimes be bolded.
Fixed a rare bug where under certain conditions the font size of the title in a formatted reference would be incorrect.
Fixed a bug that could cause citations in a group to be sorted by author incorrectly.
Refs -> New is enabled when the standalone reference window is in front.
The keyboard shortcut preference setting for Paste vs.
Paste and Match Style is remembered between launches.
References with titles containing returns will be displayed correctly in the single column view.
Fixed a bug in syncing with Bookends On Tap where one might have to repeatedly move the mouse or press a key to get the sync to progress.
Fixed a bug in the Bookends On Tap where some edited pdfs on the Mac were not transferred to the iOS device when subsequently synced.
The BibTeX conversion of several accented characters has been fixed.
Fixed a bug in the AppleScript handlers that respond to requests by DevonThink and Tinderbox in which an error was reported if the library name began with a number.
Fixed a bug where a reference transferred from one library to another by drag and drop would not be synced with Bookends On Tap.
The Greek letter ∆ is once again output correctly.
Fixed a bug in dropping multiple pdfs on a library window with the Hits group selected.

New in Bookends 12.0.1 (Jul 5, 2013)

Many functions are faster, including scanning documents and outputting XML
For Book Chapters, the format's title case setting will be applied to the Volume field as well as the Title field
Bookends will ignore a colon pasted into the Rename field by the user when attaching a file
Attachments will be exported when File -> Export References -> Export Attachments Too is checked and a bibliography format is used
Improvements in syncing pdfs with Bookends On Tap (requires BOT 2.1 or later)
The Autocomplete Paper sheet is resizable
Bug fixes and improvements:
Fixed a bug that prevented the secondary order field from being used when an in-text citation or footnote was cited more than once.
Fixed a bug that prevented scanned footnotes from displaying styled text.
Fixed a bug where cited pages were not being included when creating citations from notecards.
Importing a reference into DevonThink Pro using the Bookends template works again.
Fixed a bug that caused the Editors to be omitted when replicating an Edited Book as a Book Chapter.
Fixed a formatting problem where the punctuation between last and first names wasn't honored when the full name was output.
The menu Edit -> Copy Formatted text is properly restored after removing the selection from a notecard.
Fixed a bug that prevented keywords from being output in formatted references. Fixed a bug that could cause an entry in a Term List to be shown in RTF.
Styles assigned to punctuation in the format are now conserved when a reference is formatted.
A Return character in a format will once again be output even if the field in front of it is empty.
Fixed several bugs that prevented citation disambiguation by a letter appended to the year from working when scanning.
Improved the handling of styled text so that italics and bold text in a reference field will adopt the default bibliography format font more reliably.
The "Go To Ref" button in the ambiguous citation window that can appear during a scan works again.
Fixed a bug that caused the text in the find field in the find/replace dialog to disappear when exiting the field.
Fixed a bug that prevented Bookends from scanning long Mellel documents.
Fixed a bug that prevented Bookends from inserting the bibliography in scanned RTF files.
The text enlarge/decrease buttons for the web view in the Online Search window work again.
Emptying a field in the concise view will no longer cause an error.
Fixed a bug where "et al." would sometimes be preceded by a comma even if none was specified in the format.
Worked around a situation in which .doc or .html attachments had problems with text encoding that could cause an error message.
Fixed tabbing between fields in the Autocomplete Paper sheet.
Citations in scanned Pages documents once again include cited pages and quoted text.
Printing references works again.
Fixed a bug that could cause an error when scanning and using metatypes.
Fixed a bug in the formatter where two $ in a row would cause Bookends to consider the rest of the order field as quoted text.
Fixed a bug that could cause an error when doing a drag and drop copy of references from one library to another.
Returns are now shown properly in scanned LibreOffice documents.
Fixed a bug that caused styled text to be removed from references after a Rebuild.
Fixed a bug that could in some cases cause a question mark to be output after a unicode character in a scanned Word or NWP document.
Fixed a situation where a closing quote mark could be omitted in a citation containing cited pages.
Imports from the Online Search window will now work with databases whose extensions are hidden in the Finder.
Hanging indents work properly for unnumbered bibliographies.
Fixed a bug in hits list sort.

New in Bookends 12.0 (Jun 17, 2013)

New or Improved: 
Import references and pdfs from the Web while in the library window
Updated database engine with journaling (protects against database corruption) 
Spell checking
 Improved library window toolbar 
Advanced PubMed search lets you limit the results to a particular language (e.g. English) 
Improved detection of DOIs on Web pages Improved sorting of citation groups 
New formatting option "cap SURNAME" First names(s) will not be modified.
 New formatting option "titles in SMALL CAPS" Improved author capitalization 
Remove styles from text in reference field with a right-click 
Use Global Change if you want to do this on multiple fields and/or multiple references. 
Open attachments in the application of your choice with a right-click 
New Help menu option
Show Bookends Folder in Finder 
In the Edit Bookmarks window you can specify which Web page should be automatically opened by Bookends browser
 Right-click on a column in the reference window to select a different field to display
 Easier creation of new references from multiple attachments 
Type-ahead in Term Lists and the Groups pane
 Bookends PDF attachments that were edited in Bookends On Tap and then synced with Bookends will be placed back in their original folder  
Changed: 
Super/Sub in bibliographies no longer will end the style when a space is encountered
 You must terminate the super/subscript yourself H|2|O and ^3^H.. 
Reference exporting to versions of Bookends prior to 10 has been removed 
Reference exported to versions 10-11.3.7 will contain text but not styled text information. 
The keyboard shortcut for duplication a reference is Command-D "type" is now a reserved word in SQL searches
 To perform an SQL search for a reference Type you must enclose this word with square brackets [type] 
For the GUID AppleEvent, multiple refs will be separated by a return (ASCII 13), not a null character 
Command-M will minimize the front window 
Command-Option-M is the new shortcut for Mark/Unmark references. If the short title field is empty it will be treated as such when formatting Previously, the full title was used in this instance.
 Window -> Attachments replaces the Window -> Groups menu  
Removed: 
Import/export of EndNote 7 XML schema no longer supported 
Import/export of XML files compatible with EndNote 8 or later (including all X versions) is supported.
 Quick Font toggle 
Show Clipboard  
Bug fixes: 
Fixed a bug that would result in an error message if you dragged text onto a library window and selected Bookends Tab-Delimited File to import it.
Fixed a bug that caused an error if you invoked Copy Formatted while a field was being edited.
Fixed a bug in which a pdf shown in the reference pane was not removed when the selection changed and no reference was selected.
Fixed a bug that prevented AppleEvent searches for escaped characters from finding the correct references.
Fixed a bug that would cause an error to be thrown when doing an Autocomplete Paper with the Term List window open.
Fixed several bugs in the formatting of metatypes in scanned documents.
Fixed a bug that would yield incorrect hits when doing a boolean OR Find that was limited to references in the Hits List.
Meaningless punctuation marks at the beginning of a temporary citation will be removed from the scanned citation.
Fixed a bug that could cause an error to be thrown when scanning a .odt (LibreOffice) document.

New in Bookends 11.3.7 (May 13, 2013)

New in Bookends 11.3.6 (Mar 4, 2013)

Improvements in adding formats and import filters supplied by others:
If you receive a format or import filter from another individual or from our anonymous ftp site, you can automatically add it by double-clicking on the file or dragging and dropping it on the Bookends library window. The file will be moved to the corresponding custom folder and enabled for use. If a format/import filter of the same name already exists in the custom folder, the new file name will be modified with a sequential number and you will be informed.
A new smart group that finds the last X references entered is more accurate and much faster:
If you already have added this smart (SQL) group, delete it and reinsert it from the Add -> Smart Group (SQL) pop-up menu.
Improved Remove Duplicates:
When performing a preview and manual deletion, a red X will be displayed in the bottom pane to indicate which reference will be deleted. This indicator will change in real time if you check/uncheck references in the reference list.
Backslashes will be replaced with dashes in automatically-generated attachment names:
This is done to ensure compatibility with DropBox.
When BibTeX is enabled in preferences, the BibTeX format will automatically be enabled:
This means that if you have unchecked BibTeX in the Formats Manager, it will be checked once again when you enable BibTeX, and therefore available in format-selection pop-up menus.
Updated formats for American Society of Microbiology journals:
Also added a generic format called American Society of Microbiology that can be used instead of the individual journal formats.
In the library window column view, a tertiary sort will be performed by title if the author and date are the same:
This will only occur if the authors are shown in the first column and the date and title are shown in subsequent columns.
If "Idem" is used for a reference in a citation group, that group will not be sorted even if the format calls for it:
This ensures that the "Idem" reference follows the correct reference.
Bug fixes:
Fixed a problem that could cause a sync with Bookends On Tap to fail with an error message.
Fixed a bug that would cause an error message to appear when adding a folder to the group's pane.
An remote library that is open is now accurately detected when syncing Bookends libraries.
Fixed a bug where all items in a duplicate reference group weren't selected when doing a preview and manual remove of duplicates.
Fixed a bug where dragging and dropping a PubMed reference link from a browser onto the library window would cause an error.
Right-clicking on a pdf to open it with a specific application works again.
Warnings that a format is too new to be used by the current version of Bookends no longer appear in an endless loop.
Fixed several bugs in the use of metatypes when formatting references.
Fixed a bug in which an error could be incorrectly thrown when opening a library.
Fixed a bug in the Format Catalog that caused two examples of every reference Type to appear.

New in Bookends 11.3.5 (Jan 12, 2013)

New in Bookends 11.3.4 (Dec 27, 2012)

Autofill ISBN from any Amazon source:
In preferences, select which Amazon site (US, UK, Japan, etc.) to use to autofill references using the ISBN. This was previously limited to Amazon US. Note that many sites do not provide summary information.
Automatically exclude author and title from a citation or footnote:
If the temporary citation begins with &, Bookends will exclude the author and title (or secondary title) in the final citation or footnote.
Perform a Spotlight boolean NOT search by putting a minus sign directly in front of a word:
For example, to search for an attached pdf written by Smith and not Jones, search for "Smith -Jones" (without the quote marks).
Bookends Browser will detect DOIs on the Web Of Science web site and allow you to import references and pdfs by clicking on the green icon:
If not already present, the Web Of Science web site will be added to the Bookends Browser bookmarks.
Keywords shown in a column in the list view will be separated with semicolons:
Previously, only the first keyword was shown.
The font size delta for small caps has been changed to 3 points (from 2)
Search Web Of Science for grant number and funding agency
JSTOR parser in Bookends Browser was updated to deal with changes made by JSTOR
Bug fixes:
Improved check for a valid PMID in the PMID field when doing an Autofill From Internet. Fixed a bug that prevented text in fields being edited from being saved if some of the Action pop-up menu commands were invoked. Fixed a bug that could result in incorrect author-date sorts in citation groups if the name and date was separated by a space. Fixed a bug that caused an error when renaming a Type in preferences when a format window displaying that Type was open. The Reveal In Finder contextual menu now works in the reference pane view of the library window. Fixed a bug that could cause an error when syncing pdfs with Bookends On Tap. Fixed a problem where trying to open a pdf in Preview using the right-click hierarchical menu could result in an error. Fixed an error that could occur when changing the pop-up menu to select different search options in the Find dialog. Fixed an error that was generated with exporting a tab-delimited text file with attachments. Fixed a bug where the pdf display pane was not updated properly when replicating a Book as a Book Chapter.

New in Bookends 11.3.3 (Oct 22, 2012)

Edited pdf attachments will be synced with Bookends On Tap
Autofill single fields from the Internet:
To autofill a single field instead of an entire reference, use Refs -> Autofill From Internet -> Selected Field or right-click on that field in the reference pane (or the standalone reference window) and select "Autofill This Field From Internet". A PMID, DOI, or ISBN must be present for this to be enabled.
Web of Science searches restored:
The new search function replaces an older one that was discontinued by the service provider. If you don't have ip authentication, you can now still search the Web of Science if you have a valid username and password entered in the Web of Science import filter (Internet tab).
When tying to find a pdf online, if Bookends can't resolve the ip address it will skip to the next selected reference rather than showing an error dialog
In response to an AppleEvent asking for more than one formatted reference to be returned at once, they will be separated with a null character (ASCII 0)
Previously, they were separated with the return character (ASCII 13).
Added an AppleEvent that returns the contents of a specified field:
The Event id RFLD takes two parameters: the unique id (if more than one, separated with commas or Returns), and the name of the field to return. If the field name is unspecified or incorrect, the Title field will be returned. Field information from multiple references will be returned as a null (ASCII 0)-delimited string.
The punctuation separating authors' names is full sized when output as small caps
Small caps in author names are slightly larger
Copy Notecard and Citation will included cited pages if they occur after a header, and will not include tags
Updated the Google Scholar parser to deal with changes made by Google
Bug fixes:
Fixed a bug where dragging and dropping multiple pdfs with the Command key held down would not bring up the dialog offering to attach all to a new reference and autocomplete data if a doi was found.
Fixed a rare bug where using smart quotes could cause a hang if the field it was applied to had a large amount of text.
Fixed a problem where sorting of author-date citation groups by year would give inconsistent results if a citation included cited pages or quoted text.
Fixed a rare case where misuse of the backslash in Cited Pages could cause problems in citations when scanned with Mellel.
Fixed a bug in Subject Bibliography -> groups that could have incorrect group names shown.
Fixed a bug that prevented a straight single quote from begin converted to a smart single quote if it is the first character of a citation or a bibliography entry.
Fixed a bug where the wrong library was selected for Database Maintenance when more than one was open.

New in Bookends 11.3.2 (Aug 31, 2012)

New in Bookends 11.3.1 (Jul 30, 2012)

Convert PMID to PMCID has been updated to deal with changes made by PubMed Central
Open pdf with PDFpen added to the "Open Attachments With" hierarchical menu
When formatting, Bookends can output Ibid. (or the equivalent) in italic
Single column sort settings are remembered between launches
New AppleEvents for obtaining unique ids from Bookends libraries and performing SQL searches
Retrieve multiple references at once with the GUID AppleEvent
You can perform an autocomplete paper for only one dropped pdf at a time
BibTeX scans will recognize "\onlinecite{" as indicating a temporary citation
The temp citation metacharacter "[" will work with Mellel 3.0.1
Updated the Google Scholar parser to deal with changes made by Google
Unified format window:
The information necessary to create a custom citation is now contained in the same file as the information for creating the bibliography. Creating a custom citation is no different form creating a numbered or author-date citation (although much more flexible). Any existing formats will be automatically converted to the new scheme, and will no longer be able to be edited in Bookends 11.3 (although they can be viewed). Old custom citation format files will be obsolete. Versions of Bookends before 11.3.1 had a different user interface, and bibliography (parent) formats and custom formats were stored in different files. These older formats will be automatically converted when opened in 11.3.1 or later. If a Type exists in the parent but not the custom citation, a custom citation will be created for that type that is identical to the bibliography order. If a Type exists in a custom format but not in the parent, that custom citation Type will be ignored.
Replace authors repeated in consecutive footnotes with Idem (or your own text):
This feature works with custom citations when two consecutive citations from different works have the identical authors. It will not be invoked if the previous citation was the last in a group, and the optional sorting of a group that has a repeated citation will be disabled (so that “Idem” does change its position and follow the wrong citation).
Live Bibliography (with Mellel):
If enabled in Mellel, citations and bibliographies will be updated as you type. This feature was actually added in an earlier release, but we held back the announcement until Mellel 3.0 was released.
If a text file with the extension .ris is dropped on the library window, Bookends will offer to import it using the RIS filter:
The RIS filter must be enabled in the Import Filter Manager.
A selection of pre-defined smart groups is provided:
When adding a smart SQL group, you can choose to design it yourself (Empty), or select from a group of pre-defined smart searches (e.g. most recent 15 references added, edited in the last 2 weeks, etc.). You can also use these as templates that you modify (e.g. to find references edited in the last 4 weeks).
The maximum database cache is now 50 MB:
Levels above this could slow launch times without benefiting performance.
Bug fixes:
Fixed a bug where an "et al." in a temporary citation quoted text could result in an unmatched citation during a scan with Word or Nisus Writer Pro. Fixed a bug where doing a Find for a color label would fail. If Ibid appears in a citation group, the group will not be sorted, to ensure that the Ibid follows the correct reference. Fixed a bug where renamed field labels were not instantly updated in the library window reference pane. Fixed a bug were the modified date was not being set for references transferred between libraries by drag and drop. Fixed a bug where performing an autocomplete paper when a tag cloud item was selected could result in an error message although the autocomplete worked. Fixed a problem where some groups would not sync with Bookends On Tap. Fixed a cosmetic bug in Lion and Mountain Lion where groups didn't appear after a rebuild until the library was closed and reopened.

New in Bookends 11.3 (Jun 24, 2012)

New in Bookends 11.2.9 (Jun 1, 2012)

Import Bookends references into Tinderbox - Option-Command-drag a reference onto a Tinderbox document and it will be imported, creating a link and a formatted version of the reference, as well as populate the Reference prototype attributes with reference metadata. Requires Tinderbox 5.11 or later.
Updated the Google Scholar online search to account for changes made by Google
AppleEvent support for obtaining formatted references from Bookends
Users can use Script Editor, and developers can use an IDE, to create scripts or code that asks Bookends to return formatted references on demand. The User Guide has complete details.
Unicode normalization includes all reference fields
Modified Bookends Spotlight searches - The search is by word, with spaces between words treated as "AND"s. To do a boolean OR search, separate works with the word " or ". This replaces the old behavior, which was to treat the words entered in the search field as a phrase.
A confirm dialog will appear you edit a field in the enlarged view and press Cancel
This is a change in previous behavior, when the confirm dialog appeared when you pressed Save.
Bookends is now signed for Mac OS 10.8 (Mountain Lion) Gatekeeper
Bug fixes - Uncommitted text edits will be automatically saved when you Duplicate a reference. Fixed a bug in the format's bibliography example where the user16 and user18 default text was not correct. Show book with its chapters works again. Fixed a hang that could occur when editing additional fields in a standalone reference window. Fixed an error that could sometimes be thrown when the menu was used to bring the already opened format window to the front. Fixed an error message when importing jpgs from Amazon that would appear if the user had defined his own default attachment folder and it was subsequently renamed or trashed. Fixed a bug in the Nisus Writer Pro scan where an en dash in cited pages would not be rendered properly. Fixed a problem in Word and Nisus Writer Pro scans where an en dash in cited pages was replaced with an em dash and vice versa.

New in Bookends 11.2.8 (Apr 20, 2012)

• Updated the Google Scholar online search to account for changes made by Google
Scripts for Word 2011 SP2 (version 14.2) will be installed in the new Office scripts folder: Microsoft changed the location of the scripts folder in this version of Word.
URIs in the notes pane are active: Right-click to see the list of URIs (e.g. links to items in DevonThink or other apps). This already works in the reference fields in the Main tab.
Citation groups containing literal text will not be sorted when scanned: If any citation in a group has leading quoted text (e.g. \See also\), the entire group will not be sorted even if the format calls for it. This ensures that reference order won't be altered in a nonsensical way.
Find dialog improvement: You can now choose to search for a Unique ID directly (not as an option in text searches). The search type changes to "is", reflecting that only exact matches will be found.
Option to suppress a warning when Bookends database sync can't find the remote library: In the sync configure sheet you can turn on (default setting) or off a warning that the remote library is unavailable. Turning off this warning may be useful because it is redundant if the remote library is on a server that can't be mounted (Mac OS will display a warning in that case). If this is a common scenario for you, turn off the warning generated by Bookends.
View the references in the Hits List in their order in the library window: If you turn off sorting of the reference list in the library window (in preferences), clicking on the Hits group will show the references ordered by their position in the Hits List. If you use Hits -> Sort Hits List, the library window will be updated immediately.
The formatted reference display in the library window will update automatically when leaving edited fields
Bug fixes:
Fixed a problem with spurious characters sent to Bookends by Mellel when syncing. Fixed a rare problem that could occur if the reference Type was set incorrectly. Fixed a bug that caused incorrect scanned citations when using the 'et al. in italics' feature with cited pages. Fixed a bug where adding a reference to a static group via the menu option would cause any edited text not yet saved to be lost. The live search for "all fields" will now find entries in User19 and User20 (you'll have to Reindex any libraries made with previous versions of Bookends for this to work). Fixed a bug where the Edit menu was not refreshed properly in some cases when the note stream was closed. Fixed a bug where the ¬ character in the Misc tab text fields in an import filter was not being converted to a Return. If you limit Finds to "Any Groups", Bookends will now only show matching references that belong to one or more static groups.

New in Bookends 11.2.7 (Mar 26, 2012)

New in Bookends 11.2.6 (Feb 16, 2012)

New in Bookends 11.2.5 (Feb 13, 2012)

Notecard headers:
You can create notecards that consist of a header or have two parts, a header and content. The header will have a slightly darker color than the content and will be displayed in bolded and enlarged text. A header is created in the Notes field by placing the # character before the text (Bookends takes care of this for you if you use the command "Add Notecard With Header" (or with the note stream showing, click on the Add pop-up menu or right-click on the note stream itself). If the header has no content (that is, nothing in the line below it), it will be centered in the listbox cell. If it has content associated with it, the header will appear in the top half of the cell and the content in the lower.
New error reporting mechanism:
If you encounter an error unrelated to the database engine, you will be offered the chance to create a message in your e-mail client that contains your comments (e.g. what you were doing when the error occurred) and diagnostic information that will help Sonny Software determine the cause of the problem. Only the information you see in the e-mail message will be sent to Sonny Software.
Keyboard shortcut to add a notecard:
When the note stream is showing, Command-[ will add a new notecard and open it for entering text. The Shift-Enter shortcut has been removed.
Optional .fmt and .fltr extensions for format and import filter files:
If you use unix-based methods to transfer files between computers, the file metadata (file type and creator) will be stripped off and Bookends will not be able to recognize format and import filter files (and the file icon will be blank in the Finder). You can restore recognition by adding the extension .fmt or .fltr to the format or import filter file name, respectively, in the Finder. These extensions are optional, and for backward compatibility will not be automatically added to the format or filter names distributed by Sonny Software.
Bookends will display pdfs even if they lack a file type and/or .pdf extension
Mark/unmark all linked references in the Link Inspector at once:
Shift-click on the checkbox next to any reference or right-click and select Mark All or Unmark All from the contextual menu.
Use the down arrow key to change the search field in the Live Search box:
This is handy if you want to quickly change from one field (or All Fields) to another. Press Return or Enter to accept the new field to search (Esc or click outside the menu to cancel).
Bug fixes:
Fixed a bug in scanning Word or Nisus Writer Pro files where the open parenthesis of a citation output as a bold or bold and italicized number would assume the style of the number. Improved handling a dropped pdf proxy icon from Bookends browser on an empty reference list. The concise view background color will not revert to white when you edit a field. Importing to a specific static group by dragging a pdf from the Finder onto that group works again (was broken in a previous update). An active edited field in the reference pane is saved if the window is closed. Fixed a bug that could cause a spurious number to be output after the year when using the MLA format and final citations consisting of only the year. Fixed a bug where a notecard added to one reference could be appended to a different reference. Fixed a bug in cross-links where the default parent-child relationship was not saved correctly if it wasn't the first option (users who have set this to another option will have to check it again in preferences for the fix to work).

New in Bookends 11.2.4 (Jan 15, 2012)

New in Bookends 11.2.3 (Jan 9, 2012)

New in Bookends 11.2.2 (Dec 19, 2011)

View attachments in the library window editing pane (on the right) - The Attachments tab in the reference editing pane lets you view attachments (e.g. pdfs) on the right side of the library window. This may be preferable to the lower display pane for those with wide screen displays. If there is an attachment, it will be indicated by an asterisk in the tab panel caption (i.e. Attachment*). Note that the setting "Use WebKit to display pdfs" only applies to pdfs in the lower display pane only; the Bookends pdf viewer is always used in the editing pane.
The standalone reference window drawer has been removed - It is replaced with the same Additional Fields tab used in the library window reference pane.
There are more ways to add attachments - Refs -> Attach menu, right-click in the reference list, or use the Action pop-up menu in the library window.
The height of the lower display pane will be saved and adjusted independently for each view - This means, for example, that you can have different heights for the pdf display and the formatted reference display.
Detach has been added to the library window Action pop-up menu.
The Bookends browser data detector will check for COinS references before other types - This means that it will find all references embedded in Web pages at sites like CiteULike, not just those with DOIs.
Copy Citation button added to the library window toolbar - It works just like the Copy Selected menu: hold down the Shift key to copy without delimiting punctuation (e.g. curly brackets), the Command key to Copy Formatted, or the Control key to Copy With Modifiers.
The maximum number of references returned from Google Scholar limited to 1000 - This limit is imposed by Google.
Imports from Google Scholar are limited to 50 at a time - If you try to retrieve too many references at once, Google will think you are an automated service and block your ip address. To prevent this, Bookends limits the number of references you can import at once to 50. If you have more than 50 references to import, select and import blocks of 50 or fewer. Note that this limitation does not apply to the number of references that can be displayed (the limit is 1000), just the number that can be imported into your library at a time.
New Bookends Server options - A new parameter, HTMLOutput, lets you specify how you'd like the results of your searches returned. If it is undefined or 0 (default), full HTML output is returned. If it is set to 1, Bookends will return the results as HTML, but references, omitting the wrapping , content description data, and tags. If it is set to 2, Bookends will return the results as plain text (UTF-8) with no HTML markup. The new options may make it easier to post-process the results with your own scripts.
Bookends Server open databases names - You can open and work on a copy of your database, with the same name, as long as it is not in the Server folder.
Ad hoc control of the "before text" in cited pages - You normally tell Bookends what to output before cited pages (for example ", p. ") in the format. However, there may be times where you want to change this for a particular reference. Do this by using quoted text (text surrounded by backslashes) in the cited pages, like this: {temp cite@\: \3}. This will tell Bookends to ignore the Before text specified in the format and use a colon and space, for example: (Smuth, 2011: 3). Note that the quoted text backslash must be placed immediately after the @, and if there is no closing backslash the results will be unpredictable.
Choosing Right-click -> Copy Notecard will switch to your linked word processor and insert the selected notecards as plain text - Use Edit -> Copy Notecard to just copy the selected notecard styled text to the clipboard).
Bug fixes - Fixed a bug where using the Attachment Inspector to attach a pdf to an empty reference and autocomplete opened the reference window and did not perform an autocomplete. Fixed an error that occurred when changing the color label in the All concise view. Bookends can display the body text of Pages documents again. Fixed a bug introduced in 11.2.1 where the pop-up menu listing available formats didn't appear in the library window when viewing a formatted reference. Fixed a bug that caused erratic drawing of the browser view in the library window lower pane when window height was at its minimum limit. A standalone reference window will be refreshed once again to show a newly imported reference. Fixed a bug where an extra Enter character would be inserted in front of a Mellel temporary citation after a Verify. Fixed a bug in syncing of smart groups with Bookends On Tap.

New in Bookends 11.2.1 (Nov 20, 2011)

Bookends Browser:
detect and import references from Web pages that display a PMID or DOI
If a PMID or DOI is detected when reference surfing with Bookends Browser, the green import icon will be displayed, allowing you to view the titles of the detected references and download them. This works on any Web page that displays PMIDs (e.g. PubMed) or DOIs.
Updated direct downloads of pdfs from Nature journals and JSTOR
These fixes deal with changes made by the publishers.
Sort the single column view in the library window:
Right-click, or click on the Action pop-up, to sort by the following fields (secondary sort in parentheses): Author (Date), Title (Date), Date, Date Added, Date Modified, Type (Date). The Date Added and Modified sorts are descending (i.e. most recent at the top).
The library window title will not show the .bdb extension if it is hidden in the Finder
The library window will scroll to the reference you are entering or editing if it changes position
Updated Autofill From Internet imports reference metadata from Amazon if you have the ISBN
This was broken by changes made by Amazon.
Copy Selected without delimiters:
If you hold down the Shift key when pressing Command-Y or choosing Edit -> Copy Selected, the temporary citation that is inserted in your word processor document will not have delimiters (i.e. no curly brackets). This is useful if you want to insert a temp citation into an existing citation group.
Cosmetic improvements to the dialog window that lists multiple hits with Get PDF from local hard drive
Autosync with Bookends On Tap:
This preference, set in the Bookends On Tap Settings screen, causes syncs to begin without waiting for the confirm dialog. If you have Autosync on and want to change options in that dialog (e.g. to sync particular groups rather than all references), turn Autosync off and sync. After changing the settings in the Bookends confirm dialog and completing the sync, you can turn it on again in Bookends On Tap. Requires Bookends On Tap 1.0.2 or later.
Bug fixes:
The PubMed automated search listbox is no longer invisible. Fixed an error generated by clicking the cross-link icon in the standalone reference window. Fixed a bug where normalizing unicode in certain fields failed. Fixed a bug that could cause Bookends to crash when syncing with Bookends On Tap. Fixed a bug where clicking on the image of a Mellel document in the Attachment Inspector caused a crash. Fixed a bug that caused an error message when editing a field in the Addition Fields tab whose name had been changed. Fixed a bug where attaching of pdfs or Web pages from the Online Search window would fail if the browser was open in the lower pane. Fixed a cosmetic bug where the field labels would not be updated properly when a new reference was created with the Add pop-up menu. Fixed a cosmetic bug when the library window reference pane wasn't updated immediately after doing a Global Change -> Restore Default Font And Styles. Fixed a cosmetic issue with overdrawing of the text indicating the number of references in the library window. Fixed a bug where edited text in a field in the reference pane was not saved if the pane was closed with the View menu or keyboard equivalent. Refs -> Go To Reference # works again when the reference window is in front. Fixed a cosmetic bug when resizing the standalone reference window with the drawer open. Fixed an error in Google Search in which an author name consisting of three words or more could be displayed without spaces between the first names. Fixed a bug where a NOT search (-) in the live search box would fail in some cases when a specific field to search was specified. Fixed a bug where dropping the pdf proxy icon from Bookends Browser onto a library window would fail to import the pdf or web archive. The "date added" of a reference you duplicate is now set to the current date. Fixed a problem where Replicate As Book Chapter would give a "reference locked" error if All was not selected in the groups pane. Fixed a cosmetic issue where the reference number shown in the reference list could be incorrect.

New in Bookends 11.2 (Oct 28, 2011)

Bookends 11.2 requires an Intel Mac - Bookends 11.1.7, which runs on both Intel and PPC Macs, is still available from our Web site (http://www.sonnysoftware.com/download/download.html), but will receive no further updates or bug fixes.
Sync with Bookends On Tap - Bookends On Tap is our new app for iOS devices, and is available on the iTunes App Store. You can wirelessly sync references and pdfs between Bookends and Bookends On Tap, ensuring that your desktop and portable libraries are up-to-date.
Reference entry/editing pane integrated in the library window - The editing pane can be opened in a variety of ways (Refs -> New, double-clicking on a reference or selecting a reference and pressing Return, clicking on the Edit Reference button at the lower right, and the Views menu). A Preferences setting allows you to revert to the old behavior, opening references in a separate window.
New browser pane in library window - If the selected reference has an entry in the URL field, clicking on the URL icon (globe) at the bottom of the library window opens a browser in the lower pane showing the corresponding Web page. The browser is active, meaning you can follow links and navigate to the full text or a pdf of the reference. You can attach whatever you are viewing (a pdf or a web page as a webarchive) by clicking on the attach icon (paper clip) associated with the browser.
Single column reference display - A "column" control lets you display the reference information in multiple columns or a single column. The single and multi-column views are functionally identical (i.e., mark references, drag and drop, right-click contextual menus, etc.).
Two new fields: Medium and User20 - These are available in the Addition Fields tab (or the drawer in the reference window). The Medium field is intended to hold the type of publication (Print, Video, Internet, etc.), which is required for the MLA 7th edition format.
Attach folder contents with drag and drop - Drag and drop folders on a library window with the Command key down attaches any files in them (and in any subfolders).
Window -> Reset Window Position - Although Bookends tries to ensure that the library window is visible when you move from a two display setup to one display, sometimes the window is drawn off screen. If this happens, use Window -> Reset Window Position to move the main window (or the reference window, if it is not integrated into the main window) to the top left corner of the main screen.
If Bookends doesn't find a recently opened library on opening, it will ask you if you want to create one - You can always create a new library at any time with File -> New Library.
Indicate references that have orphaned attachments - When you right-click on the references list or click the Action pop-up button, you can choose to indicate references with attachments that can no longer be located. Bookends will indicate these with red paper clips. The next time the reference list is redrawn the paper clips will be drawn normally.
Open an attachment in Preview or Skim - These options are in an "Open Attachment With" hierarchical menu generated by right-clicking on an attachment in the lower display pane ("Use WebKit to display pdfs" must be unchecked). The default option opens the attachment in the application the Finder chooses.
Each library window remembers its own settings when reopened - As a result, Bookends works more smoothly with the Lion option to restore window positions when re-opening apps.
Library Maintenance -> Verify checks for unnormalized Unicode and offers to normalize and reindex - Unicode normalization is performed if necessary when you do a Database Maintenance -> Rebuild or Repair. Unicode normalization is also performed if necessary when older databases are converted to 11.2. Normalize for Pages, Volume, Date, Location, Publisher, User 1-4.
Improved Remove Duplicates - If two references are otherwise identical, the reference that belongs to a static group will be retained.
Improved Find and Replace - This function (in Global Change) no longer opens the reference window to allow find/find next/replace next, but works globally on the selected references, the Hits List, or the entire database. You will be told how many references will be affected before confirming the replace operation.
The factory default link type is Book : Book Chapter - This can be changed in Preferences. Undefined link types are no longer allowed.
Many small cosmetic changes
Library window nomenclature - To simplify documentation and comparisons between Bookends and Bookends On Tap, your collection of references will be referred to as a library, not a database, throughout the documentation.
Smart scanning of UTF-8 encoded text files - Bookends will recognize a UTF-8 BOM at the beginning of a text file and correctly interpret accented characters. If no BOM is detected, Bookends assumes the file is encoded in MacRoman.
You can create sql searches for Date Added (example in User Guide)
Create final superscripted citations that have a closing but no opening parenthesis - This format is used by journals published by the Japan Society for Bioscience, Biotechnology, and Agrochemistry (JSBBA). This feature is not yet available for Mellel documents.
The Refs -> Find Again menu has been removed - All Finds result in putting the matches in the Hits List. The option to replace or append to an existing Hits List remains but the popup menu giving the choice will be disabled if there are no hits, in which case there is nothing to append to.
The Go To Reference menu and keyboard shortcuts work when the library window is in front - Note that First, Last, Next, Prev refer to the actual reference number in the database, not to the place in the sorted list of references.
Removed menus: Peek, Insert Reference, Hits navigation when the library window is in front
Removed controls: the library window View pop-up and the + add reference button
Removed features: BibTeX option to underline labels of required fields (color field is still available)
Bug fixes - Fixed an issue with how an ellipsis is displayed in Google Scholar online searches. Fixed a bug that caused excessive CPU use when the List View window was open. Bookends will no longer generate an error message if text is mistakenly entered when searching for a reference by a unique id. Fixed an incompatibility with Lion that caused an error when trying to scan an OpenOffice .odt document. Fixed a bug where autocomplete paper with JSTOR would not import the metadata. Fixed a rare error that could occur when scanning with metatypes and a reference has an undefined link type. The default attachment subfolders popup menu is now updated correctly if the subfolder has been deleted in the Finder. Fixed a bug where proofreading a Word document would remove a leading ^ in a temporary citation. Fixed a bug where author names placed in front of the final citation by using the ^ metacharacter didn't obey the name formatting rules if a custom citation format was used. Fixed a bug that could cause conversion of author names to Normal case to fail in some cases. Fixed a bug where cited pages following styled text would assume that style. Fixed an error that could occur when the reference list was unsorted and a key was pressed. Links to DevonThink records now work in the reference pane URL field after a right-click.

New in Bookends 11.1.7 (Aug 29, 2011)

Direct searches of Amazon Italy and Amazon China  
Import total pages and edition from Amazon, if present   
Amazon will allow you to retrieve no more than 100 references for a given search  If a search finds more than 100 hits and the book you wanted is not in that list, you must refine the search. This is a new limitation enforced by Amazon, not Bookends.   
Normalize Unicode  Bookends stores text as composed Unicode. If you enter decomposed characters (for example, by copy and pasting text from the Web), indexed searches (such as Live Search or Find Words Beginning With) can fail to find some or all of the matching references because the decomposed characters interfere. Database Maintenance -> Reindex, Rebuild, and Repair functions will now normalize any decomposed characters found in the following fields: Authors, Editors, Title, Keywords, Notes, and Abstract.   
New smart quotes: Swedish Print  Example: »double quote» and ›single quote›   
Words with embedded apostrophes can be added to the list of words whose case should not be changed  
Output a close parenthesis after scanned citations  Some publications require citations consisting of a superscripted number followed by a close parenthesis. This option is available in the format definition "Enclose citations with" pop-up menu.
Bug fixes:
  Fixed a rare bug where an attachment could be attached to the wrong reference.
Fixed a first-run installation or update bug where the Formats folder could be empty.
Fixed a cosmetic bug where the fomat pop-up at the bottom of the lower pane could disappear.
Fixed a rare bug that could cause quoted text from the last citation in a paper to be inserted in the first citation after a scan.
Changed the cited pages function so that it will not try to expand or contract a page number in a range if more than one page range, separated by a comma, is entered in the pages field.
Fixed a bug in scanning Pages documents with annotations that could result in a hang.
Fixed a bug that caused some unicode characters to be displayed incorrectly in a bibliography after scanning.

New in Bookends 11.1.6 (Jul 19, 2011)

New in Bookends 11.1.5 (May 16, 2011)

A new metacharacter to automatically change parentheses to square brackets
If a citation begins with a square bracket, Bookends will replace any internal parentheses with square brackets when scanning with a custom citation format. This is useful for formats such as SBL, where footnotes following quotes are surrounded by parentheses, and the parentheses that would normally be used inside the footnote should be changed to square brackets. This feature does not work yet with Mellel.
Updated the JSTOR Bookends Browser importer to be compatible with changes made by JSTOR
Access Google Scholar Related articles in Online Search
To see Related articles, hold the Option key down when you select a reference in the Online Search window and you have toggled to the Web view (lower pane). This can be useful if you have access privilege for the pdf from some sources and not others. In the Related articles web page you can chose to get the article from a source for which you have privileges.
Cited pages are ignored when a format calls for numbered citations
This setting is in Preferences, Refs tab. If the reference has no title, the author and date will be used.
Use literal text with more than one citation in a citation group in Word and Nisus Writer Express
Previously this was only possible with Mellel and Pages.
If a citation group contains literal text at the beginning, the group will not be sorted during a scan
This prevents the leading literal text from (such as "See also") from being moved in the final formatted citation group.
You can now access formats in the Custom Formats folder when running in the demo mode
Note that if you currently use Bookends 9 or earlier, any format you open or use will be automatically updated to the Bookends 11 schema and can no longer be used by the older version.
Bug fixes:
Fixed a bug where "Ibid." was left out when scanning with a custom citation format.
Fixed a bug where an error could occur for some author-date scans.
Fixed a bug that could cause incorrect footnote citations with cited pages, and failure to make a range of consecutive number citations, in Word and Nisus Writer Pro scans.
Fixed some issues where punctuation preceding cited pages was not trimmed properly.
Fixed a bug where an error could be thrown if PubMed or Library of Congress search contained certain punctuation marks.
Fixed a bug where cited pages used with numbered citations could result in incorrect output.
Fixed a bug in the JSTOR import filter that prevented it from importing journal name and volume.
Fixed a bug that caused the second of two consecutive citations to the same work with different cited pages to be empty when scanning with the MLA format.
Fixed a bug where unmatched citations would not be listed after a Word or Nisus Writer Pro scan and the unmatched citations would be emptied.
Fixed a bug where dropping the pdf proxy icon from the Bookends Browser window on the Finder didn't create a copy of the pdf or webarchive.
Fixed a rare bug that could result in ∆ to appear at the beginning of references in bibliographies.
Fixed a bug that could cause a Word or Nisus Writer Pro document to be truncated after scanning with a format specifying "Use year-only for repeated authors".

New in Bookends 11.1.4 (May 16, 2011)

Expanded support for APA 6th - For references with 8 or more authors, Bookends will output an ellipsis after the sixth author and follow it with the name of the last author, as required for the APA 6th style. The placement and composition of the text can be modified for other styles if needed.
Copy notecards - Use the standard Edit -> Copy (Command-C) to copy the text of the selected notecards to the clipboard. This is useful if you want the notes but not the temporary citation. Copy Notecard is also available via the right-click contextual menu.
New location for formats from Sonny Software - The factory-supplied Formats folder will be moved to ~/Library/Application Support/Bookends/ with each update. When Bookends is updated, the contents of the old Formats folder will be replaced with the latest versions shipped by Sonny Software. Any formats you have created or modified will not be touched (they will be in the Custom Formats folder). This change was introduced to make Bookends compliant with Mac App Store rules.
Automatically rename an attachment with the reference title
This setting is in Preferences, Refs tab. If the reference has no title, the author and date will be used.
The file format of the Microsoft Word 2008/2011 script files has changed
Improved importing of references from CrossRef - Worked around a problem in CrossRef where the text encoding of the reference metadata from CrossRef was misrepresented to Bookends.
Bookends will prompt you to create a database on first run - The prompt will appear when you click on the Continue Demo button and there are no databases in the Open -> Recent Database menu.
Increased font size in Format Manager examples - The styled citation example in the format definition window will be 2 points larger than the bibliography default, to make small characters like punctuation easier to read when creating/editing formats.
Bug fixes:
Fixed a bug in import and attach from a pdf's doi if the metadata was provided by CrossRef.
Fixed a bug where an extra parenthesis was output when scanning an RTF file with citations beginning with quoted text.
Fixed a bug where drag and drop importing of a Google Scholar reference could result in appearance of garbage characters if the default import encoding wasn't set to UTF-8.
Fixed a bug where a Find for characters in a specific field could return incorrect references.
Fixed a problem with rename attachment where the presence of certain characters in the name could cause a crash.
Fixed a bug that could cause incorrect MLA citations with some word processors when the same reference was cited consecutively.
Fixed a bug that could result in failure to update the "Save PDF to Bookends" option for new versions (does not apply to Bookends bought from the Mac App Store, which does not allow automatic creation of these files).
Improved algorithm to display the number of references in the subset when doing a live search.
Fixed several issues where some footnotes in a Pages document would be overlooked during a scan.
When creating a new virtual tag with a right-click, pressing Cancel exits without creating a virtual tag.

New in Bookends 11.1.3 (Feb 27, 2011)

Search for phrases, including punctuation, with Live Search - Live Search normally searches for indexed words, which is very fast but doesn't allow searching for phrases or punctuation. If you enclose text in the Live Search box with quote marks, Bookends will search for an exact character match. For example, searching for "United States" will not match a reference that has the words "United Kingdom" and "altered states", only ones with the exact proper noun (the search is still case-insensitive). You can mix indexed and non-indexed searches. To perform a NOT search, place a minus sign immediately before the opening quote mark, for example: cancer -"B cell lymphoma" will find references with the words "cancer" but not "B cell lymphoma". Once you type in a quote mark, Bookends will wait until you've entered a closing quote mark before performing the search (that is, Bookends won't perform a search if there are unbalanced quote marks). Note that non-indexed searches are slower than indexed searches, which you will notice if you have many references. Bookends will display a spinning progress wheel to indicate that a non-indexed search is being performed.
Insert a notecard's content and its citation in Mellel - Requires Mellel 2.8.1 or later.
Improved PubMed automated search - Any references found by the search that you already have in your database will be colored yellow. Various cosmetic improvements were made to the automated search window.
Import text encoded as UTF-16 - Set this in the File -> Import Text Encoding menu.
Updated functions that use CrossRef, such as importing from existing bibliographies - Deals with changes made by CrossRef.
Display text of attached Mellel 2.8 and later documents - Works with the compressed file format introduced in Mellel 2.8.
Changes in Import Filter and Formats Manager windows - If there are two formats or import filters with the same name (one supplied by Sonny Software, one in the Custom Format folder), only the custom format will be shown in the corresponding manager window.
Bug fixes - Fixed a bug where updated Word 2011 AppleScripts would failed to install automatically. Fixed a bug that prevented COinS from being detected. Fixed a bug in author-date scans using ibid when consecutive citations of different references were output as year-only and were from the same year. Fixed the JSTOR filter and reference detector. Fixed several problems in Bookends browser. Fixed a bug in PubMed automated search that caused a crash if no Bookends database was open. Fixed a bug were some attachments with Unicode characters were not found by the "Reveal In Finder" function.

New in Bookends 11.1.2 (Jan 31, 2011)

New in Bookends 11.1.1 (Dec 19, 2010)

New in Bookends 11.1 (Nov 26, 2010)

Introducing virtual tags:
Virtual tags allow you to group tags words in titles, abstracts, and/or notes under a term of your choosing. For example, you could create a virtual tag Colors and include in it the terms red, green, and blue. The size and color of the virtual tag Colors would reflect the frequency of all of these tags, and when you click on Colors… in the tag cloud pane Bookends will display all the references that have any of those words in the corresponding fields. You can also use virtual tags to aggregate words with the same basic meaning but differ in tense or spelling, such as computer, computers, computerized, etc. You can tell Bookends to hide or show individual tags that are included in a virtual tag. You can manage virtual tags in two places, Preferences (Tags tab) and in the tag cloud pane (via contextual menus). In the latter, select and then right-click on a virtual tag to see the tags it contains, remove an individual tag component, or delete the virtual tag. Select one or more real tags and use a right-click to add the selected tags to an existing virtual tag or to a new virtual tag you create on-the-fly.
Attach a PDF only if reference metadata is found online:
This option is available when attaching PDFs in bulk by dropping them on a database window with the Command key held down. If the box “Attach PDF only if reference metadata are found online” is checked, Bookends will only attach a pdf (and move or copy it to the default attachments folder if requested) if Bookends can locate the reference metadata on the Internet. This is useful if you want to have Bookends automatically download reference data for pdfs you already have, but don't want the pdf attached if Bookends can't locate it.
Amazon online searches will display book descriptions, if present:
These will be imported to the Abstract field.
A sortable publication date column has been added to the Amazon search display
Set the maximum number of recently opened databases Bookends will display (Preferences)
Get PDF works with more publishers
Get DOI was updated to work with changes made by CrossRef
Improved handling of Ibid. citations:
To avoid ambiguity, if a citation is the last member in a group and then is cited immediately after that group, Ibid. will not be used even if the format calls for it.
Database Maintenance -> Rebuild (Keep User Settings) has been named Rebuild:
The old Rebuild function, which deleted all database-associated information and groups has been removed. If there are problems with database tables, you can use Database Maintenance -> Repair instead to fix them.
Bug fixes:
Fixed a bug in the Mellel scan where Ibid. could be incorrectly used for identical consecutive citations to different references, or an error message could appear. Fixed a bug in the Pages scan where text could be mistakenly repeated in the scanned document. Fixed a scanning bug where an open parenthesis could be mistakenly be output when citation enclosures were suppressed and the citation began with quoted text. Fixed a bug that could cause a letter to be appended to the year after scanning with Word or Nisus Writer Pro if a document had only one citation. Fixed a minor bug where Live Searches could result in a list of references where none was selected. Fixed a bug in groups where renaming a folder could result in failure to update its subgroups. Fixed a bug in Mellel scans where using Ibid. could result in an error. Fixed a bug in which a proofreading scan of a Word or Nisus Writer Pro file could introduce a spurious open parenthesis. Fixed a rare bug that could result in the inclusion of spurious unicode characters or punctuation in a citations after a scan. Fixed a bug where incorrect groups could be listed in formatted references. Fixed a bug where "et al." could sometimes be output with the wrong text style. Fixed a bug that could in some cases cause a scanned NWP document to be truncated after an inserted pdf image.

New in Bookends 11.0.9 (Sep 19, 2010)

New in Bookends 11.0.8 (Sep 6, 2010)

Direct JSTOR searches and using JSTOR for autocomplete paper restored: This was broken by changes made by JSTOR. Note this still requires ip authentication.
Searching for and importing JSTOR references and pdfs with Bookends Browser restored: This was broken by changes made by JSTOR. Note that automatic downloading of JSTOR pdfs still requires ip authentication.
CrossRef added as a source for Autofill: Bookends will attempt to autofill a reference (Refs -> Autofill From Internet) based on a doi from Internet sources in this order: PubMed, CrossRef, Google Scholar. Because CrossRef is usually a better source than Google Scholar, this should improve the completeness and quality of the metadata.
Korean and other Asian characters returned with a Google Scholar online search are rendered correctly
Microsoft Word scripts are compatible with Microsoft Word 2011
Revised handling of modified journal glossaries: If you modify a journal glossary that's in Bookends 11 Folder/Journal Glossaries, Bookends will ask you to rename it when it is saved. The renamed copy will be saved to ~/Library/Application Support/Bookends/Custom Journal Glossaries and be set as the default journal glossary. This ensures that the glossary will not be overwritten when you upgrade Bookends.
Improved handling of selected references: Bookends will remember the last selected references when you move away from a group and then return to that group. This does not apply to the group Hits or to virtual groups (made from selected multiple groups).
Smart quote options now include German Guillemets: Examples: »double« ›single‹
Bug fixes:
Fixed a bug in Term List where updating the list would ignore any text in the search filter. Fixed several cosmetic errors in the standalone Term List window. Fixed a bug where an opening citation parenthesis would not be output when scanning a Word document with a format calling for italicized numbers, and where using the "don't enclose citation" metacharacter, *, would result in the inappropriate output of the open parenthesis. Removed the "Show Examples of All Formats" button from the format window (use Biblio -> Create Format Catalog).

New in Bookends 11.0.7 (Aug 8, 2010)

Create a catalog displaying all your formats - Biblio -> Create Format Catalog will generate a file containing examples of each Type from each format. The catalog can contain all formats, only formats marked in the Formats Manager, or just the default format. The catalog will automatically be opened in the application used to open RTF files (usually TextEdit). Format catalogs are especially useful for finding a format whose output is similar (or identical) to one you need but for which a specific format does not exist. Note that unlike most real-life examples, the example references used by Bookends have no empty fields, so the output may contain reference information that you won't usually see with your own references. Also note that hanging indents will not be shown in the format catalog, and that metatype formats will output example fields from the same reference regardless of any parent/child (i.e. square bracket) indicators.
If the temporary citation delimiter has been set to comma for use with BibTeX, it will be reset to semicolon if BibTeX is disabled - This ensures that you won't get spurious citations when scanning temporary citations with commas, such as {Smith, 2010, Nature}.
Improved attachment indicator - Multiple attachments are indicated by two paper clips in the List View. This replaces the red paper clip that was introduced in Bookends 11.0.6.
Allow selection of any file when importing references - The File -> Import References dialog allows you to view text files or all files. This is useful if you have downloaded a file from the Internet that cannot be identified as a text file (e.g. it doesn't have a .txt extension or the TEXT file type metadata). Note that you can also import such a file by drag and drop with the Shift key held down.
Drag and drop multiple files change - The default behavior is now to attach each file to the selected reference. If the Command Key is held down, Bookends will offer to attach each file to a new reference.
Footnotes created with a custom citation format and that contain super- or subscripted characters will be displayed correctly in scanned Pages documents
Link Inspector change - The parent : child relationship is now only based on the settings in Preferences (Links tab). That means that the reference you display in the Link Inspector "dock" can be either a parent or a child, and relationships you set with references in the link list will act accordingly.
Use drag and drop to import PubMed references from Google Chrome - This feature has always been available for Safari.
Bug fixes -Fixed a bug that could insert a space before the title in some references imported from JSTOR via Bookends Browser. Fixed a bug that could affect formatting of conditional groups that contain the issue field. Fixed a bug in scanning where letters were sometimes not added to the year to disambiguate identical citations referring to different references. Fixed a bug in Sync where specifying Use Last Sync Dates could result in the wrong Client/Master relationship. Improved the reliability of of Spotlight searches within Bookends. Fixed a bug that could cause an existing attachment to be detached when copying a new file with the same name to the attachments folder. Fixed a bug where an extra parenthesis could be output when using quoted text with a citation that will be output as an italicized number).

New in Bookends 11.0.6 (Jul 11, 2010)

Attach multiple files to the same reference in one drag and drop - Press the Command key when making the drop. If you don't press Command, Bookends will offer to attach each file to a new reference.
Import multiple text files with one drag and drop - Press the Shift key when making the drop. If you don't press Shift, Bookends will offer to attach each file to a new reference.
Automatically rename attachments by title - If selected in Preferences, Bookends will use the first 220 characters in a reference's title when it automatically renames an attachment.
Improved author "ignore list" for sorting - The author "ignore list" used for bibliography sorting can include punctuation marks used for grouping: (, [, and {. For example, you can enclose an author's name in parentheses, such as (Smithy, JR) and the reference will sort with others that have author names beginning with 's'.
Drag and drop import to a specific group - If you drag a text file to a static group and import the references, those references will be automatically added to that group. If you drop a pdf on a static group and chose to Autocomplete Paper, the imported reference will be added to that static group. If you drop a pdf on a static group and do not autocomplete pape, the pdf will be attached to the selected reference in the list, as usual.
Footnotes created with a custom citation format and that contain super- or subscripted characters will be displayed correctly in scanned Pages documents
Improved attachment indicator - A red paper clip will be displayed in the List View to indicate that a reference has more than one attachment (otherwise a grayscale paper clip will be used).
Bug fixes:
Fixed a bug in which styled text could be incorrectly formatted in footnotes inserted in a scanned Nisus Writer Pro document.
Now you can search Google Scholar for exact text by surrounding multiple words with quote marks.
Fixed a rare problem where an extra space could be output after a surname when using a format calling for "et al." to be inserted.
When Copy Formatted is used with a linked Pages document, the formatted reference will be automatically inserted but in plain text — manually paste if there is styled text in the formatted reference.
Fixed a bug where bibliographies generated from scanned OpenOffice documents could only be created with plain text.

New in Bookends 11.0.5 (Jun 7, 2010)

Globally rename attachments - Refs -> Global Change -> Rename Attachments will automatically rename any attached files in the selected reference, the Hits List, or the entire database according to the specifications defined in Preferences. This is similar to the rename attachment option available in the Attachment Inspector or right-clicking on an attachment in the List View window, but can be applied to many references at once. This operation is not undo-able. Note that if an attachment is shared by two databases, changing its name will make any links to it in other databases orphans.  Automatically rename the pdf after autocompleting a paper - The autocomplete paper dialog sheet has an option "Rename pdf after import". If checked, after importing a reference Bookends will rename the attachment according to the specifications you defined in Preferences.  Attach multiple files to new references in one step - If you drag and drop more than one file onto the List View or reference window, Bookends will offer to attach each one to a new reference. This is a convenient way to populate your reference database with pdfs you already have. Bookends will look for an embedded doi in any pdf you drop, and if found will try to download the reference metadata from PubMed or Google Scholar. You will be able to specify if they will be moved or copied to the default attachment folder (or subfolder) or left in place, and if they should be renamed. Names will be generated according to your preference settings. Note that the reference's metadata, if found, will be used to create the name. If not found, generic placeholder names will be created.  The ~/Documents/Bookends folder can be deleted by the user if it is not being used - It will be automatically recreated if you use the Bookends automatic backup feature (highly recommended!) or move attachments to the default attachments folder. This is intended for those few who don't use these features and who want to keep their Documents folder "tidy".  Extended the ability to exclude particular titles from title-case rules - To exclude a Series Title, Short Title, or Book Title from the title-case rules for a format, end the text with a comma (this already works for the Title field).  Footnotes created with a custom citation format and that contain super- or subscripted characters will be displayed correctly in scanned Pages documents  Improved List View sort - Bookends will use the first author for sorting if only the first author's name is shown (set in Preferences). This means that the references will appear in first author-date order.  Restored the ability to import references from existing bibliographies via CrossRef - This had been broken by changes made by CrossRef.org.  File -> Import From Existing Bibliography is a menu item - This will take you to CrossRef Simple Text Query, just as Online Search -> Bookends Browser does. It has been added as a menu item for convenience and visibility.  Improved handing of text files after import - If you have checked "Move to Trash after import", Bookends will move the file to the Trash only if at least one reference was imported. Therefore, if you use the wrong import filter by mistake, you don't have to recover the file from the Trash to try again.  Bug fixes - Choosing Mark/Unmark All when the Terms List is being viewed in the List View will only affect the references showing in the reference list (the same behavior as when Groups are showing). Fixed a problem in Snow Leopard that caused Bookends to fail to display pdfs in the List View window when WebKit was turned off or in the reference window. The Term List filter textbox is now cleared when the Term List to be displayed is changed. Fixed a bug that would cause link relationships to not display in the Inspector in certain circumstances. Fixed a bug in HTML export that would trigger an error message if the first author position of a paper was an empty line. Fixed a bug where dashes could be inappropriately substituted for an authors name if it was from a chapter in an edited book and the edited book was included in the bibliography just before it. Eliminated a leading space that could be present when adding a term from a Term List to an open reference window. Fixed a bug where a citation could be garbled when scanning a Mellel document and output "et al." in italics turned on in the format.

New in Bookends 11.0.4 (May 6, 2010)

Display Term Lists in the List View window - The Groups pane header is now a pop-up menu from which you can select Groups or a Term List (Authors, Keywords, etc.). Clicking on a term will show all the references in which it is contained, and selecting multiple terms will show the references that contain all of the terms (AND) or any of the terms (OR), as specified in the Action pop-up or a contextual menu. The Term List window still exists, but now is just a single column that can be used to rapidly add one or more terms to many references at once, change a term's spelling, be saved as a text file, etc.
Updated database engine - Some operations are faster than in previous versions. Custom formats created in Bookends 7 and never modified in a later version will not be recognized by the newer database engine.
Journal Glossary and Term Lists menu items have been moved to the Window menu
The Extras menu has been removed.
Bookends creates a new alias in the PDF Print Services folder each time it is launched - This means that the alias won't be broken by upgrading to a new version of Bookends.
Restored Get DOI functionality - This was broken by changes made by CrossRef.
Improved pdf download to handle changes made by some publishers
Keyboard shortcuts let you add/change reference ratings - Using Shift-Option-Command-# to assing ratings (0 through 5 stars).
The Find and Find In This Reference dialogs are now sheets rather than windows
Bug fixes - Fixed a rare bug that could cause custom citations to be malformed if they contained Unicode text. Fixed a bug in Autocomplete Paper that could result in an inappropriate error message. Fixed a problem introduced in 11.0.2 where Bookends would not match temporary citations containing accented characters. Fixed a bug where filling in the PMCID from the PMID on multiple references at once could result in incorrect pairing. Fixed a bug that could cause the "get references from existing bibliography" to hang. Fixed a minor bug involving color labels. Fixed a bug in scanning .odt files created by NeoOffice. Fixed a bug that could prevent syncing of a Mellel document with a Bookends database. Other minor fixes.

New in Bookends 11.0.3 (Apr 12, 2010)

Add terms (keywords, authors, etc.) to multiple references in one step - Open the Term List window and drag one or more terms onto the List View window. Bookends will offer to add those terms to the selected references. If the term is an author, editor, or keyword, Bookends will check to see if it is already in the corresponding field of each selected reference, skipping over it if the term is present. This operation can also be invoked with the Action pop-up menu or right-click contextual menu "Add Term To Selected References". If the reference window is open, this option will be worded "Add Term To Open Reference".
Better identification of references you already have when performing an Online Search - Bookends will use the doi (if present) in addition to the pmid to determine if you already have a reference when searching PubMed.
Run attached QuickTime movies (.mov) in the List View window display panel.
Right-click on Online Search references to select those you do or don't have - You can then import or delete the selected references.
Easily add tag cloud words to the "stop list" list of words to exclude - Add selected tag cloud words to the stop list via the Action pop-up menu or right-clicking and selecting the corresponding contextual menu choice. This works with Title, Abstract, and Notes tag clouds.
Improved pdf download to handle changes made by some publishers - Previous versions could return a "103" error in some cases.
Bug fixes - Fixed a rare bug that could cause custom citations to be malformed if they contained Unicode text. Fixed a bug in Autocomplete Paper that could result in an inappropriate error message. Fixed a problem introduced in 11.0.2 where Bookends would not match temporary citations containing accented characters. Fixed a bug where filling in the PMCID from the PMID on multiple references at once could result in incorrect pairing. Fixed a bug that could cause the "get references from existing bibliography" to hang. Fixed a minor bug involving color labels. Fixed a bug in scanning .odt files created by NeoOffice. Fixed a bug that could prevent syncing of a Mellel document with a Bookends database. Other minor fixes.

New in Bookends 11.0.2 (Mar 22, 2010)

Import journal articles in existing bibliographies - In some cases Bookends is able to locate and download articles (and pdfs) listed in existing bibliographies. To do this, use Bookends Browser to go to the bookmarked CrossRef simple text query page (http://www.crossref.org/SimpleTextQuery/). Paste in a bibliography copied from a word processor document or pdf, one reference per line. If PMIDs or DOIs for one or more reference is identified, Bookends will show a list of the titles and you can choose to import them (with or with looking for the pdf) into your Bookends database. Bookends will attempt to retrieve the reference metadata from PubMed or Google Scholar. Because the process only finds references that have a DOI or PMID listed in PubMed or Google Scholar, the chances of success are much greater for journal articles, especially those in the biomedical literature, than for other reference types. Even for these, you should not expect 100% efficiency. This is especially true of older articles in the biomedical literature that do not have their DOIs entered in PubMed, which means that Bookends relies on Google Scholar for the metadata, which unfortunately sometimes returns the wrong article.
Retrieve PubMed Central ID (PMCID) - If a reference has a PMID, you can use the menu Refs -> PMID -> Fill In PubMed Central ID (PMCID) to have Bookends search for the PMCID. This can be done in batch by selecting multiple references in the List View (the first must have a PMID for the menu to be enabled). There is a limit of 2000 PMIDs that can be processed in a single query. When used in the List View, Bookends will report the number of PMIDs that were submitted and the number of PMCIDs that were found.
Get PDF From Internet is better at finding older biomedical articles
The Links button in the reference window is always enabled - If there are no links the color is dark gray, if there are links the color is blue. Clicking on the Links button toggles the Links Inspector.
Output page ranges with "Last page as entered" - If this is selected in the format (Bibliography tab), Bookends will not try to parse non-standard page ranges. For example, 5.14-15 would be output as is, not expanded to 5.14-5.15. You can have Bookends output the "Last Page As Entered"on an ad hoc basis if you terminate the pages in the Pages field with a comma. In this case, Bookends will always output the page range exactly as it was entered regardless of how page ranges are set to be handled by the format (Bookends will still output just the first page if the format uses "p" rather than "p-").
Exclude a title from the format's case rules on an ad hoc basis - If a title ends in a comma it will be output as entered regardless of what case rules (Title Case, ALL CAPS, Sentence Case) are specified in the format.
Output square brackets ( [ and ] ) in metatypes by entering them as quoted text (i.e. surrounded by two dollar signs, backquotes, or tildes)
PDFs are displayed in the reference window with Bookends’ built-in controls, and the reference window appearance has slightly changed - As a result, the text cursor will no longer submarine (disappear for a short period of time) when using the arrow keys to navigate in text fields.
Bug fixes - Fixed a bug where accented characters at the beginning of a source field could be mangled when imported. Fixed a bug in which the italic style could be incorrectly offset within a citation group in a scanned Pages document. Fixed a bug where renaming a group in a folder would cause it to disappear when the folder was closed and reopened. Fixed a rare problem where importing multiple references at once form some sites (e.g. ICCU) could fail. Fixed a bug in metatypes where the pages for the first (child) reference might be output even though the temp citation containted cited pages. Fixed an issue when scanning Mellel documents where special citaiton formatting instructions, such as output date-only, were ignored if the citation was to have no enclosing punctuation. Fixed a problem where the live search textbox would lose the focus after a few keystrokes if "Use WebKit to display pdfs" was enabled.

New in Bookends 11.0.1 (Mar 8, 2010)

New in Bookends 11.0 (Feb 15, 2010)

New in Bookends 10.6.4 (Feb 1, 2010)

New in Bookends 10.6.3 (Dec 27, 2009)

New in Bookends 10.6.2 (Dec 15, 2009)

Import references and pdfs from PubMed On Tap (an iPhone/iPod Touch app) - PubMed On Tap is a product of References On Tap, which can be purchased from the iTunes App Store. PubMed On Tap lets you search PubMed and store reference information and downloaded pdfs on the device. If the iPhone/Touch is on the same local network as Bookends, you can view the references in the PubMed On Tap library and transfer them, with pdfs if present, to your Bookends database. Bookends will display the references you already have in your database in yellow, or filter the references so that you see only those you don't already have. Here is a link to PubMed On Tap in the iTunes App Store.
Copy Attachment Path - You can copy an attachment’s full pathname to the clipboard by right-clicking on it in the List View window and selecting "Copy Attachment Path" (this will not work if you use WebKit to display pdfs). You can also use the Action gear in the Attachment Inspector.
Downloading pdfs from from online sources works with more journals
Search the Notes tab in the reference window with "Find In This Note" and Find In This Note Again"
Improved formatting of date-only citations - If a date-only citation is included in a citation group and scanned with custom citation format, Bookends will use a comma to separate the reference from a preceding reference, regardless of what character is normally used to separate references. This means that if you create a citation like {Smith, 2005 #12324; %Smith, 2009 #3434; Jones, 2006 #23243}, Bookends might output (Smith 2005, 2009; Jones, 2006).
Improved BibteX scanning - If you have BibTeX enabled and Copy Citation is set to copy the Key field, when scanning Bookends will only check to see if a temporary citation is present in the Key field. This will prevent Bookends from misidentifying temporary citations as ambiguous when the citation's text is present in other fields in other references.
Improved notecards - Rendering and saving a notestream is orders of magnitude faster, meaning that it is now feasible to have hundreds of notecards in a stream.
Citations created during a scan of a Word document will not change subsequent text to the style of the style sheet
Improved import of XML files exported from Papers
The default Type of an imported reference can be set in the import filter (Misc tab)
This was previously possible only for references output as MARC records, and the default import Type for others was the same as the default Type for a new reference. Now the default Type for a new reference and for an imported reference can be different.
Improved Change Case -> Title Case - If there is a period, colon, question mark, or exclamation point followed by a space, the character after the space will be output in uppercase even if the word is in the "do not change" list. Thus, a title might look like "Ben Hur: The Sequel".
Bookends Tutorial.pdf and the video tutorials available on the Sonny Software web site are accessible from the Help menu Bookends Tutorial.pdf must be in the same folder as Bookends.
The preferred location for Bookends User Guide.pdf is now in the Bookends 10 Folder This is where Help -> User Guide will look for it. If not found, Bookends will look in the alternative location, ~/Documents/Bookends/ folder (for backward compatibility).
Added Cut/Copy/Paste to the right-click (contextual) menu for text fields
Bug fixes - Find In This Reference works when the reference window is in front. Japanese and other Unicode characters in a Google Scholar search result are now rendered properly. Corrected formatting problems when names with suffixes (e.g. Jr.) are being output in small caps, or when first names/initials are surrounded with parentheses or square brackets. Fixed a bug where a scanned document could be truncated after a citation if the final citation was numbered and in styled text. Fixed a bug in the Attachment Inspector where renaming an attachment would always apply to the first attachment even if another was selected. Authors/editors names imported from MARC records will retain a period after the last initial, if present in the record. Fixed a bug where accented characters in some Google Scholar imports could be scrambled. Fixed several issues dealing with fonts. Fixed a bug that would cause final citations in a scanned Word document to not adhere to the local style sheet settings. Various fixes for scanning citations in Pages footnotes. Fixed a bug in the Online Search data detector display where line spacing was too narrow, making it difficult to read the reference titles. If requested in the Online Search window, Bookends will attempt to download the pdf for an imported reference even if the reference isn't shown in the List View (e.g. if there is text in the Live Search textbox and the imported reference didn't meet that criterion). When a reference is being formatted with the Book Chapter[Book] metaType, the format setting for "Replace repeated authors with" will apply only to the Book Chapter, not the Book. Fixed a formatting bug with author names when only editors were to be output with "et al.".

New in Bookends 10.6.1 (Oct 16, 2009)

Nisus Writer Pro integration - Bookends now communicates directly with Nisus Writer Pro (NWP) 1.4 for citation insertion, scanning, and rescanning (or unscanning). NWP 1.4 has an Edit -> Insert -> Bibliography menu, and the options therein initiate interactions with Bookends: 1) Switch To Bookends, 2) Find Reference (in Bookends), 3) Insert Citation (from Bookends), 4) Insert Bibliography Placeholder, 5) Scan Document (with Bookends), 6) Unscan Document (with Bookends). If you choose to retain hidden citations when you perform the scan, you can rescan the document (or unscan it) at any time. The macros that were previously provided for interaction with Nisus Writer Pro and Express are no longer supported.
Improved importing of reference metadata from Bookends Browser - If you drag and drop the pdf proxy icon onto a Bookends database window, you'll have the option to import the pdf (or web page) to a new empty reference and automatically initiate the Autocomplete Paper process. You can also right-click on the pdf proxy icon and select "Attach To New Empty Reference And Autocomplete Paper". Use these methods to download pdfs or webarchives and allow Bookends to try to find and import the reference's metadata from the Internet.
Press Escape to clear the text in any Search field
The Action menu or a right-click lets you deselect all unpinned terms in a Term List window
Use Shift-Option, not just Option, to highlight in yellow the groups to which the selected reference belongs - This was previously accomplished by pressing the Option key alone.
Automatic downloading of the User Guide - The User Guide is included in the manual Bookends download. When Bookends is run, it will move the file "Bookends User Guide.pdf" to ~/Documents/Bookends, where it will be found if you use the Help menu.
Improved MLA formatting - If consecutive citations are from the same work, only the cited pages will be used in the second case.
Updated autocomplete paper using Google Scholar - Accented characters are displayed and imported correctly,
Bug fixes:
Fixed a bug that could cause a crash when performing a Copy Citation with Mellel as the linked app in Mac OS X 10.4 (Tiger).
Fixed a cosmetic bug in the List View window after a Term List window had been opened.
The Stop button works when formatting references for printing. Performing a Copy Citation when linked to Mellel works properly in Tiger (broken in Bookends 10.6).
Fixed a bug that could cause some temporary citations in Word to be garbled.
Fixed a bug in which citations in some Pages footnotes would be missed.
Fixed the names for the fields "After surnames" and "Between names", which were reversed in the format definition window.
Fixed a bug that could cause smart groups to sometimes include a reference that it shouldn't.
Fixed a bug that cause the enclosing citation parentheses to be omitted when scanning a Pages document with the MLA format if the final citation included the italicized short title.
References can be deleted when the Attachments group is selected in the List View window.
If a citation in a group is to be formatted as year-only (preceded by a %), the group will not be sorted when using a custom citation format that would otherwise sort the citations.

New in Bookends 10.6 (Sep 14, 2009)

New update notification mechanism in Snow Leopard - Sparkle automatic updating is disabled when running in Snow Leopard because of incompatibilities. Bookends will still provide automatic checking for updates and the Check For Updates menu will function. If a newer version of Bookends is found, a dialog will offer to take you to the download page on our web site, where you can download the new version and install it manually (which means simply replacing your old Bookends 10 Folder with the new one).
Resize the list of terms and display of matching references in a Term List - Term List filters - Filter which terms you see in real-time by typing in characters in the term list filter. Bookends performs character matching, so that the characters "cog" will match the keywords "cognitive science" and "neurocognition".
"Pin" terms in a Term List - If you click on the pin image next to a term, it is temporarily "pinned" and treated like a selection (until unpinned, or the term list is dismissed). You can accumulate terms in this fashion to perform boolean AND/OR searches. When multiple terms are selected or pinned, the actual search Bookend is performing is shown. You can pin or unpin all terms with an option in the Action menu or by right-clicking on the term list.
The AND/OR setting for finding multiple selections in Term Lists is remembered between launches
When multiple terms are selected (or pinned), Bookends will display the boolean search being performed
Create a hypertext link from more than one notecard - Select the notecards you want then use Edit -> Copy Notecard As Hypertext Link, or drag and drop them with Option-Command held down.
Add text to a new reference directly from a pdf when using Autocomplete Paper
If you cannot find the reference online when you choose Autocomplete Paper, you can fill in the reference fields using the Action pop-up menu. Select the text and use the pop-up menu to tell Bookends which field it should be placed in. The selected text will replace any text that might already be in that field. If the text is sent to the Authors, Ser. Editors, or Translator field, Bookends will assume it contains names and will rearrange it accordingly. It will assume that words separated by commas represent names, and that the names are surname-last. Bookends will also remove punctuation not normally association with names, as well as numbers and common superscript symbols. Click the Close button when finished.
Copy Citation And Modifiers menu - When you invoke Edit -> Copy Citation And Modifiers (Control-Command-Y) or click on the Copy Citation button with the Control key held down, Bookends will prompt you for the page or page range you want to cite, and other possible modifications to the temporary citation. If there is any selected text in the frontmost window, Bookends will use that as the default value for Cited Pages. If you click OK or press Return, Bookends will switch to your linked word processor and insert the temporary citation with the cited pages at the end, e.g. {Carpenter, 2008, #12343@12-14}. You can also tell Bookends what text (if any) you want to precede the citation or if you want the citation treated in a special manner after the scan (such as show date only, excluded the cited reference from the bibliography, etc.). If more than one reference is selected, cited pages will be applied to the first citation in the group.
Italicize 'et al.' in citations created with an Author-Date scan - Enabled in the format definition window, Citations tab.
Generate Subject Bibliographies based on smart groups - When you select Group while creating a subject bibliography, both static and smart groups will be shown. Both types of group can be used in the same subject bibliography.
Formatting examples update automatically when a reference is edited and then the format window is brought to the front
APA 16th Edition format
Refs -> Global Change -> Remove Orphaned Attachments - Removes an attached file from a reference if the file cannot be located. It can be applied to the selected references, in the List View, the Hits List, or the entire database. This is not undo-able.
If the List View has a DOI column, it will be instantly updated after performing a Get DOI - The Preferences settings for font sizes are comboboxes - You can enter a point size not listed in the pop-up display.
Bug fixes - Fixed a screen refresh issue that could cause a pop-up menu in the list view to flicker. Fixed errors that could occur when scanning when the format definition window was in front. Fixed a bug that could result in incorrect Book Chapter [Book] metatype output if two or more such citations were found in the same citation group. Fixed a bug that allowed unnumbered bibliographies to have a hanging indent only when scanning Word documents. Fixed a bug with the Book chapter [Book] metatype where a hanging indent could cause a return character to be added to the bibliography entry when scanning with Word. Fixed a bug that could make it seem that unlinked references that had nested unique ids were actually linked. Fixed a bug that caused umlauted characters in temporary citations in Nisus Writer Pro documents to be duplicated. Accented characters in subject bibliographies generated by scanning from Word are rendered correctly. Fixed a situation where trying to download a pdf from a Springer site without access privileges would result in an error message rather than failing silently. Fixed several small cosmetic issues in the Preferences window. Updated Amazon.de search so that it works after changes made by Amazon.

New in Bookends 10.5.6 (Aug 6, 2009)

New in Bookends 10.5.5 (Jul 12, 2009)

Updated Google Scholar online search and autocomplete paper - Changes made by Google required an update in the parsing engine.
Updated the Get PDF feature to deal with changes made by certain publishers
Improved detection of doi's in pdfs when attaching files
You can select and manipulate multiple notecards at once - This can be particularly useful if you want to copy multiple notecards at one time to another application, such as a word processor or email application.
Improved MLA format - If a Book short title is required to disambiguate citations, it will automatically be output in italic (if there is no short title, the title will be used).
When importing pages, Bookends will strip out certain trailing characters - These are " p", " p.", " s", and " s."
The ambiguous citation/citation not found window is a regular document window - Unlike the old floating palette, this window will be visible if you switch to your word processor to locate the temporary citation in the document.
Reference metadata copied to the clipboard from OpenOffice Writer can be imported into Bookends
Global Change -> Change Case will properly apply Title Case to words having an apostrophe near the beginning
For languages such as French, contractions such as d' and l' in front of a noun should be left as lower case. When using Title Case, Bookends will treat the apostrophe as a word break character unless it occurs prior to a word-terminating letter "s" (the possessive case). This is already handled properly when a reference is formatted for a bibliography or footnote (see what’s new in version 10.5.4, below).
Improved handling of footnotes in Pages ’08 and ’09 documents - Bookends will find and insert footnotes in scanned Pages documents if they are reset at the beginning of each page or section, and if they are denoted by Roman numerals or symbols rather than Arabic numerals.
Bug fixes
Fixed a cosmetic bug affecting the List View scrollbar refresh.
Fixed an error that could occur when printing a bibliography directly to a pdf.
Fixed an issue where editing a format in the Formats folder would actually update a format of the same name in the Custom Format folder.
Fixed a bug in a Pages '09 document scan where a temporary citation in a table was recognized but not replaced.
Suggested file names when rebuilding or repairing databases will take into account the database extension, if any.
Spotlight searches in the List View window work again.

New in Bookends 10.5.4 (Jun 19, 2009)

Book chapter [Book] metatype - This “metatype” allows you to combine information from a book chapter and book in a single footnote and/or bibliography entry. Such a citation might look like "Smith, The way things are, In: Jones (ed.) 2009. p. 12-34", where the first third is taken from the book chapter, the second from the book that contains it, and the last from the book chapter again. You can tell Bookends to use the metatype when a certain number of chapters cite the same book. Bookends will automatically add the book to the bibliography if it is not explicitly cited in the text (it is implicitly cited when the book chapter is cited).
Exclude citations from the bibliography - If you place a $ immediately after the open temporary citation character (usually the open curly bracket), after a scan the final citation will will appear in the text or a footnote, but not the bibliography.
COinS metadata will be embedded in the bibliography returned by Bookends Server, if selected in Preferences.
This means that those using Firefox to access your database will be able to directly import the references from the browser into their Zotero databases.
Option-double click on citation group in Mellel will cause all members of the group to be made hits and shown in the Bookends List View window
Get PDF From Internet works with more publishers
If you right-click on the Title field and it has a selection, Bookends will offer to put the selected text in the Short Title field
Scripts for Apple Pages - Go To Bookends, Find In Bookends, Insert Citation From Bookends, Scan Open Pages Document In Bookends. These scripts can be accessed while you are running Pages via the Scripts menu on the right side of the menu bar (it's an icon, not a word). If you don't see the Scripts menu, you can enable it by running AppleScript Utility and checking "Show Script menu in menu bar". If you are running Bookends for the first time, these scripts will be automatically installed in ~/Library/Scripts/Pages. If you have run Bookends before, you'll need to move the scripts there manually.
Increased the time Bookends will wait for a DOI to be returned (Get DOI) before it stops trying, resulting in a greater success rate
Improved Title Case handling - For languages such as French, contractions such as d' and l' in front of a noun should be left as lower case. When useing Title Case, Bookends will treat the apostrophe as a word break character unless it occurs prior to a word-terminating letter "s" (the possessive case). Therefore, for the examples above, entering the letter d or l in the list of words to be unchanged when applying Title Case would cause a word such as "d'etat" to be output as "d'Etat".
When creating a new Bookends database, the suggested name will include the extension .bdb
Minor cosmetic changes.
Bug fixes - Fixed a bug that could cause some custom citation formats to use the secondary order when the reference was being cited for the first time. Fixed a problem whe using Title Case in a format where a word's case is mistakenly change when it follows certain punctuation, such a period or semicolon. Fixed a bug in smart search where searching for empty DOI or PMID fields, or for a reference's unique id, would fail. Fixed an error that occured when getting a DOI based on a book's ISBN. Doing an advanced PubMed search restricted to Random Controlled Trials works again. Fixed several bugs in Finding references but not putting the results into the Hits List. Fixed a bug that would cause scanning of the open Pages '09 document to fail. Scan Open Apple Pages Document now works on PPC Macs. The metacharacter for "don't include final citation in the bibliography" (!) works with Pages '08 and '09 documents. Fixed a bug that could cause a crash when scanning with a format that groups references that are always cited together. Fixed a rare but where a spurious character could be introduced into Japanese Word 2008 documents after a scan. Fixed a problem where files not on the startup volume were left on that volume after being copied to the Trash (e.g. when automatically trashing an imported file, deleting a format, or deleting an import filter).

New in Bookends 10.5.3 (May 4, 2009)

Nested group folders:
Create a group and folder hierarchy in the List View window with unlimited sublevels.
If a folder or a group is selected, a newly created group will be placed in that folder or after the selected group.
A new folder folder is created at the end of the Groups list.
Hold down the Option key when clicking on a folder's expand/collapse triangle and all subfolders in that folder will be expanded or collapsed.
This is a convenient way to quickly show or hide all of the items a folder contains.
Older databases are updated automatically to the new groups structure (internally) when opened in Bookends 10.5.3 or later.
If these updated databases are reopened in older versions of Bookends, the groups will appear outside of any folders they may have been in.
Flatten groups list hierarchy:
The List View action pop-up menu under the groups list (or a right-click in the groups list) allows you to "Flatten Groups List Hierarchy".
This will cause all of the groups and folders to be listed at the root level (that is, no subfolders).
This may be useful if the groups list becomes disordered and you want to reveal all of the items in it so that you can rebuild the hierarchy.
This function is not undo-able.
Automatically obtain a reference's doi:
The menu Refs -> Get DOI will request the reference's digital object identifier (doi) from CrossRef.
If found, the doi will be added to the selected reference(s) in the List View window or to the reference showing in the Reference Window.
CrossRef requires that some reference fields have accurate information, including author, journal or book title, first page, year of publication, and article title.
The doi can then be used for features such as Autofill and Get PDF From Internet.
Indicate JSTOR references already in your database:
After performing a JSTOR online search, any references that you already have in your database will be highlighted in yellow.
Bookends uses the JSTOR URL to identify references.
After an Online Search, quickly go to a reference you already have in your database:
Select a reference that is highlighted in yellow (meaning it already exists in your database) and right-click.
Select Find Reference In Database (Shift-Command-J) from the contextual menu to have Bookends locate that reference.
Increase/decrease HTML text size in Bookends browser.
Use a pop-up menu in access bookmarked sites in Bookends browser:
The “bookmark” icon (a small blue ribbon) brings up a list of sites you have bookmarked so you can quickly reference surf to them.
You can edit/add bookmarks with this menu.
The same functionality can be accessed with File -> Go To URL, but the local pop-up menu is more convenient.
Scan an open Apple Pages '08 or '09 document from within Bookends:
If Pages is open, Bookends will enable a menu Biblio -> Scan Open Apple Pages Document.
If the document has never been saved, Bookends will offer to switch to Pages so you can save it.
If the document has unsaved changes, Bookends will offer to save the file before doing the scan.
If you choose not to have Bookends do this, the scanned and formatted document will not include the unsaved changes.
Automatic update of User Guide when using Sparkle:
When using Sparkle to update Bookends, the new User Guide will be downloaded replace the old (if present) in ~/Documents/Bookends/.
Open online references with a right-click from the reference window:
Right-clicking in the doi or pmid fields in the reference window drawer will allow you to select a url that will open the article or PubMed entry in your browser.
If you invoke Autocomplete Paper in the List View and don't find a match, Bookends will open the (usually empty) reference in the reference window for manual data entry.
If you click the Attachment tab in the Inspector floating window, Bookends will display the attachments of the currently selected reference.
Best-guess detection of ambiguous citations during a scan:
If a temporary citation is ambiguous, Bookends will assume the first word is an author's name and scroll to and highlight the first match in the ambiguous citations dialog.
For example, if the citation is (Smith 2009} and there are two possible matches, one where the first author is Smith and another where the second order is Smith, Bookends will highlight the former.
You can of course then select either.
The ability to save searches from the SQL/Regex search window has been removed.
This function was superseded by SQL smart groups.
Bug fixes:
Fixed a bug that caused JSTOR searches to behave erratically.
Fixed a bug that could cause Bookends to crash when scanning some Pages documents containing complex images.
Fixed a bug that interfered with scanning when "group references always cited together" or "sort groups by year" is enabled.
Fixed a bug in scanning of Pages and Mellel documents where quoted text in one citation could be placed in a succeeding one if the temporary citation didn't have a match.
The sort direction arrow indicator is now set correctly in the List View if you are sorting the [Date] Added column.
Fixed a bug where the Rename Attachment feature in the List View window would suggest a name derived from a reference other than the the first selected.
Disambiguated MLA citations using the short title will enclose it in quote marks if the reference is a journal article or book chapter but not if it is a book.
Fixed several issues with finding the correct reference when Option-double-clicking on a temporary citation in Mellel.

New in Bookends 10.5.2 (Apr 5, 2009)

New in Bookends 10.5.1 (Mar 30, 2009)

Autofill references from Internet:
Automatically import or update reference metadata in articles and books. If the first selected reference in the List View (or the one in the reference window) has a PubMed ID (pmid), Digital Object Identifier (doi), or ISBN, the menu Refs -> Autofill From Internet is enabled.
When invoked, Bookends will use the pmid, doi, or isbn to find the reference metadata (author, title, etc.) and fill in the corresponding fields in the reference. Bookends will try to find the reference on PubMed first (even if you only have the doi), and if the reference is not there will try Google Scholar.
If the reference has an ISBN and no pmid or doi, Bookends will use it to find the book on Amazon.com. This option also useful for updating references, especially those in PubMed, whose metadata can change after the initial electronic publication. The menu PubMed -> Update From PubMed has been removed (the function is included in Autofill From Internet). The menu Refs -> Lookup From DOI has been renamed Refs -> Lookup Article From DOI.
Import a reference from the Internet by drag and drop of a doi:
If you drag and drop the doi of an article on a database window, Bookends will create a new reference and search PubMed and Google Scholar to find it and import the metadata. The doi *must* begin with the characters "10." (without the quote marks), and only the doi must be present in the drag.
File -> Export Attachments:
This menu will be enabled when the first selected reference in the List Window (or the reference in the reference window that is in front) has attachments.
Bookends will create of a copy of each attachment (in the case of the List View window, for each selected reference that has attachments) in the selected destination folder.
The original attachments will remain where they were. An attachment will not be copied to the destination folder if the folder already contains a file with the same name.
Export references and their attachments:
When you use File -> Export References (Hits), a checkbox gives you the option to export any attachments they contain as well.
Export rules are the same as for Refs -> Export Attachments.
Attached text files can be edited:
If an attached text file is displayed in the List View window lower pane or the reference window Attachment tab, you can edit it.
When leaving the field (e.g. by tabbing) you be asked if you want to save the changes.
Note that if the text file is open in another application it may not be possible to save the changes.
Reorder attachments:
Multiple attachments are normally listed in the order in which they were added.
You can change that order by rearranging (via drag and drop) the names in the Attachment Inspector list.
Color labels can be applied the text or the background:
The colors in the color label designations can be used to color the text or to color the background of the references in the List View.
This choice can be set in Preferences.
The default for existing users is color text, and for new users is color background.
The date or date and time format used by the import filters matches that of Refs -> Insert Date
Attach and display password-protected pdfs
New link type: Original:Translation:
This will appear only when for new installations of Bookends. For existing Bookends users, you can enter this relationship in Preferences (Links tab).
Increased minumum database cache to 10 MB
Added a warning when the user tells Bookends to use a format to create temporary citations (Preferences)
The setting of the "Trash after import" checkbox in the import dialog window is remembered between launches
If you attach a .zip file, Bookends will not unzip it when you choose "Open Attachment"
Improved citation disambiguation for the MLA format:
When scanning with a format such as MLA that disambiguates citations by short title, the short title will appear without surrounding quote marks and in italic, if you have set it to italic in the reference. If there is no short title, the full title will be output in quotes.
Bug fixes:
Fixed a rare instance in which scanning a Pages document that has Section Breaks and has been edited and then imported from Microsoft Word on Windows would result in an unreadable formatted document.
Fixed bugs that prevented Bookends from coming to the front when a dialog scan was initiated in Word or Mellel and that could cause problems when Ibid. was used in some formats.
Periods terminating abstracts are no longer removed when importing MARC records.
FIxed a bug where the progress dialog would not close after rebuilding an empty database.
Fixed a few problems with some formats would cause the addition of disambiguating information to citations to fail or be incorrect.
Fixed a problem with scanning a Pages document where control symbols (%, -, etc.) immediately after the opening citation delimiter weren't recognized. Bookends will attach a pdf to an empty reference and perform an autocomplete paper correctly even if a group is selected or there is text in the live search box.
Using a dash (-) in front of a temporary citation to exclude authors in a citation group works on a citation-by-citation basis (just like % does to show date-only). You can no longer delete the group "Attachments". Fixed a bug in scanned Pages documents where the tabs in lines with multiple tabs could be out of order.

New in Bookends 10.5 (Mar 11, 2009)

Note streams and notecards - The contents of the Notes field can be divided into virtual notecards that can be displayed and manipulated separately. Create a stream in the Notes field by separating individual notes with two Returns (a single empty line between the notes). In the List View window you can show the note stream by clicking on the Note Stream icon at the bottom right or by appropriate menu/contextual menu. Each notecard will be displayed in a scrolling list. Use the + button (or Shift-Enter) or the - button (or the Delete key) to add or remove a notecard in the note stream list (hold the Command key to avoid the warning dialog). Edit a notecard by double clicking on it or selecting it and pressing Enter. Save the edited notecard by clicking the Close button or pressing Enter. To abort press the Cancel button (bottom right) or press Escape. Reorder notecards by drag and drop. Copy a notecard's contents along with a temporary citation to the reference with Edit -> Copy Note And Citation. You can also drag and drop the notecard with the Option key held down into a word processor window. If you use Copy Citation or Copy Note And Citation and the notecard begins with cited pages (@ followed by the page(s)), Bookends will include the cited pages in the temporary citation. For example, if the notecard is "@7 This is my note.", Bookends might create a temporary citation like this: {Smith, 2009, #123432@7}. If you are using Copy Note And Citation, the cited pages will be removed from the beginning of the note. A contextual menu that let's you access many of these functions with a right click, as well as select any URIs/email addresses in the notecard. You can even paste a “hypertext link as text” from one reference into a notecard of another and right-click to navigate between them. If you drag and drop text from a pdf or any application onto the notes stream, Bookends will create a new notecard for it. Set the font, font size, and color for notecards in Preferences.
Use EZProxy with Bookends browser and reference surfing - If your institution uses EZProxy you can access restricted web sites even if you are off campus. Enter the EZProxy URL in Bookends Preferences (Internet tab)—it must end in %@ or it won’t be recognized. To start an EZProxy session, open Online Search and either perform a search in Bookends browser or with Google Scholar or PubMed (not JSTOR or Web Of Science, which require ip authentication) and then click on the Web toggle icon to surf references. You will be asked for your name and password, and then taken to the article's web site. You can navigate to the article's pdf and use the Import With PDF import option. For direct download of pdfs from these sites (that is, without using Bookends browser/reference surfing), you still require ip authentication. If you leave the proxy space (the URL doesn't include the proxy information), you can start it again by clicking in the URL field and pressing Return, or press Option-Command-L. Note: EZProxy is for HTML-based access. It will not allow you to perform direct searches of restricted sites—you need to be on campus or have a VPN client for that.
Live e-mail address links in the concise view - Clicking on such a link will open your e-mail client and insert the address. In the reference window, right-click on a field containing an e-mail address to display it in a contextual pop-up, preceded by "mailto:". Selecting this will open your e-mail client as well.
Display files inside an attached folder in the Attachment Inspector
Import references/pdfs from the Online Search window with a right-click contextual menu
Bookends will strip any trailing non-letters from names when importing
Updated Bookends browser JSTOR data detector
Show all chapters in the same book - If a Book Chapter is selected in the List View or shown in the Reference Window, Refs -> Show With Chapter will show all of the chapters from the same book. This already works with Books, Edited Books, and Conference Proceedings.
Bug fixes:
Fixed a bug that could cause scanned citations in Mellel documents to be incorrect.
Dragging and dropping a reference from the online search window onto a static group once again adds the reference to that group.
FIxed a bug in which final citations in footnotes of scanned Pages documents could appear more than once.
Fixed a bug that could cause an error when copying and pasting text from one field to another.
Fixed a rare bug that could cause an error when scanning with a format that alphabetized grouped citations.
When moving a file to an attachments folder on a server, a copy of the original will not be left behind.
Fixed a bug that caused an error to be thrown if you edited a format with an unregistered copy of Bookends (i.e. the demo).

New in Bookends 10.4.4 (Feb 11, 2009)

Scans will find citations in tables in Pages '09 documents - Scanning already works with Pages '08 tables.
Browse to select subfolders in the default attacment folder - When attaching a file, you have the option to select a subfolder in the default attachments folder hierarchy with a "select folder" dialog. This may be faster than using the pop-up list if you have many subfolders and sub-subfolders. If you select a folder outside of the default folder hierarchy, you will receive an error message. If you create a new folder with this dialog, make sure its name is unique in the default folder hierarchy or Bookends may not be able to find attachments in it.
Copy/paste smart groups - In the List View, select a smart group and click on the Action pop-up menu or right-click on the group list to bring up then contextual menu option "Copy Smart Group". Chose the Action pop-up menu or right click again and the option to "Paste Smart Group" will appear. The smart group may be pasted into the same database to duplicate it, or into another database to copy it. If the group name is already used, a number will be appended to the name of the pasted version to make it unique.
Edited formats and filters are automatically moved to their custom folders - If you modify a filter or format, it will be immediately moved to the corresponding custom folder in ~/Library/Application Support/Bookends. This ensures that your modified filter or format will be retained when you upgrade to a new version of Bookends. If a filter or format with the same name is already in the custom folder, the modified file will not be moved.
The names of the static groups to which the references belong will be shown in the manual remove dups side-by-side comparison
Preferences -> Override system proxy settings - Bookends normally accesses System Preferences to get your proxy settings (if any). If you want Bookends to use a different proxy setting from the rest of your applications, check "Override system proxy settings" in Preferences (Internet tab) and enter the proxy server address and port that you want Bookends to use. This setting will be used by Online Search but not by Bookends browser (reference surfing), which always uses the settings in System Preferences.
Remove paths to arbitrary attachment folders - Bookends stores the paths to any folder in which you have attachments if they are outside of the default folder. On occasion this can cause problems, for example a very long pause as the Finder tries to locate a folder on a server that is no longer available. In such cases you can clear the internal list of paths with this option in Preferences. Note that you will have to reattach one file for every folder if you want to reestablish the path. This does not apply to any attachments in the default folder or its subfolders—they will always be found.
Bug fixes - Fixed a bug that could cause scanned citations in Mellel documents to be incorrect. Dragging and dropping a reference from the online search window onto a static group once again adds the reference to that group. FIxed a bug in which final citations in footnotes of scanned Pages documents could appear more than once. Fixed a bug that could cause an error when copying and pasting text from one field to another. Fixed a rare bug that could cause an error when scanning with a format that alphabetized grouped citations. When moving a file to an attachments folder on a server, a copy of the original will not be left behind.

New in Bookends 10.4.3 (Jan 15, 2009)

Bookends can scan Pages '09 documents saved as flat files (the default) or as packages
Automatic updating of Bookends works again if you have Bookends 10.4.2 or later
Open URLs or URIs linking to other applications from within Bookends:
Right-click on any field in the reference window that contains a URL/URI to bring up a contextual menu containing that hyperlink.
This will allow you to, for example, use links to items in DevonThink 2 and access them while you are in Bookends.
If the URI is in a field that normally contains multiple lines of text (e.g. the Abstract field), it must reside on its own line or Bookends won't recognize it.
Application URIs (e.g. to DevonThink 2) will also appears as live links in the concise view pane.
Attachment subfolder hierarchy is cached:
The list of attachment folders/subfolders shown in the Attach Dialog pop-up menu is cached after the first time the window opens.
If you have a complex attachment subfolder hierarchy, this will make opening the window considerably faster.
If you create a new subfolder, the cache will be automatically updated.
If you bypass Bookends and add/delete an attachment subfolder the Finder, use the menu item "Rebuild Folder List" to update the pop-up menu.
These URIs will also appear as live links in the Concise View pane.
Send your documents to Bookends as pdfs to be attached - A menu item "Bookends" will be added the Print -> PDF pop-up menu of all applications. The “printed” pdf will sent to Bookends, which will allow you to attach the reference to the first selected reference or a new empty reference (if the List View is in front), or to the reference showing in the Reference Window (if it is in front).
Bug fixes:
Citations in Pages and OpenOffice documents beginning with modifiers such as *, %, and - are now processed correctly.
Fixed a cosmetic but where editing a reference in the right pane of the List View window would generate an error message if the List View contained a Links column.
The Attachment Inspector now shows the the selected reference's attachment, if there is one, when it opens.
Fixed a bug that affected the ability of the up and down arrows to display all the relavent terms when using autocomplete in the reference window.
The Online Search text search field is no longer disabled when switching from a boolean search to a Google Scholar search.
Fixed a bug in scanning an Apple Pages document with a format that uses year-only to disambiguate two citations.
The concise view scrollbar resizes correctly if necessary when changing references in the List View.

New in Bookends 10.4.2 (Dec 27, 2008)

New in Bookends 10.4.1 (Dec 15, 2008)

Reference cross-links (links):
Establish relationships between references with the Links Inspector.
The selected reference in the List View (or the open reference window) will be made the "parent" and appear in an image well above the linked list.
To add a link, drag and drop one or more references from the List View (or the unique ID in the reference window) onto the Inspector link list.
Choose a link relationship with the parent (e.g. Review and Work Reviewed) as well as add comments.
Double-click on a linked reference or the parent reference to select it in the List View.
Use the checkbox next to the reference to add or remove the reference from the Hits List.
If you have viewed more than one parent, forward and back arrows let you scroll through the viewing history.
You can define up to 20 link relationships in Preferences and indicate which is to be used by default (if any).
You can see which references have links, and how many, by selecting "Links" as a List View column in preferences.
The reference window has a Link icon which will be enabled if the reference has links.
Click on the enabled icon to open the Link Inspector and make this reference the parent.
Control format output with conditional groups:
You can tell Bookends to use the information in a given field in the formatted reference, and if that field is empty to use another field.
"Conditional groups" are enclosed by curly brackets, and the conditional fields are separated by the caret, ^.
You can place as many conditional separators as you want, and you can include punctuation and quoted text in the conditional statements.
For example, if you wanted the title output in quote marks, and if no title was present the journal name output, and if neither are present the publishers name preceded by the label "Published by", you could use this construct: {"t"^j^`Published by `u}.
The logic is: if there is a title output it in quote marks, if there is no title output the journal name, if there is no journal name output the words "Published by " followed by the publisher's name.
If there is more than one field in a conditional group, *all* must have data or that group will be ignored.
If a format order begins with an editor (e.g. an Edited Book), Bookends will punctuate the editors’ names as specified for authors
Bibliographies will be placed at the end of scanned RTF file after the first scan
If you are doing a rescan of an RTF document and retain hidden citations was enabled, the bibliography will be placed wherever you had previously moved it. Subject Bibliographies are placed in the clipboard, to be pasted into the scanned RTF file after opening it in your word processor.
Word RTF documents can be rescanned
You can choose to "Retain hidden citations" when you scan an RTF file.
If you do, you can rescan the document and Bookends will incorporate any changes you have made and generate new final citations and a bibliography.
Note: this option only works with RTF files created by Microsoft Word.
If you open and save the scanned RTF file with another word processor (e.g. Nisus Writer, Mellel, etc.) the hidden citations will be discarded.
Unscan a Word RTF document:
You can unscan Word RTF file that you have previously scanned with "retain hidden citations" enabled.
The result of the unscan will be an RTF file in which final citations and the bibliography have been removed and temporary citations have been restored.
Note that you can rescan without doing an unscan first.
Attachments can be placed in an unlimited number of subfolders in the default attachments folder:
To create new subfolders, when adding an attachment select the "parent" folder from the folder pop-up menu and then select "New Folder".
The default subfolder (if any) will be saved and restored per database (that is, you can configure different databases to use different default attachment subfolders).
Rename attachments:
You can tell Bookends to rename an existing attachment.
When you do, any reference in the database that attaches that file will be updated to reflect the new attachment name.
Note that this will break links to that attachment, if they exist, for references in other databases.
Rename attachment can be invoked in the List Window action pop-up menu, by right-clicking on the image of the attachment in the List View attachment pane, or in the Attachment Inspector.
Reattach option:
If an attachment has been renamed in the Finder and Bookends can no longer locate it, you can select "Reattach" from the List Window action or a contextual menu that appears when you click on the attachment pane. Once a file has been reattached, the obsolete name will be removed from the reference.
Improved Bookends' ability to correctly identify DOIs embedded in pdfs.
You can have grouped citations ordered by date when scanning with a custom citation format.
If the final citation contains no text before a cited pages entry, any spaces or punctuation at the beginning of the "before cited pages" text will be suppressed.
Show books with their book chapters:
If the reference window in front, or the first selected reference in the List View is a book, edited book, or conference proceedings, the menu Refs -> Show With Chapters will be enabled (in the List View you can also right-click or use the Action menu pop-up).
When selected, Bookends will find and list the book and any chapters it has (they are identified as such if they are of Type Book Chapter and have the book's title in their Book Title field).
Bug fixes:
Fixed a bug that could cause the scan of a Pages or OpenOffice document to hang if there are cited pages in a citation and no "before" cited pages punctuation entered in the format.
Fixed a bug where right-clicking on the proxy icon in Bookends browser could return an error.
Modified the JSTOR data detector in Bookends browser to account for changes made by JSTOR.
Fixed a bug where pressing the Option key would fail to identify smart groups that contained the selected reference when the smart group specified which other groups the reference belonged to.
Fixed a bug introduced in 10.4 where the name punctation for a custom citation was taken from the format used for scanning, not the custom format.
Fixed a bug where double-clicking on an attached folder could create a copy of the folder.
Fixed an SQL error that could occur when selecting an empty group with the Attachment Inspector open.
Fixed a rare occurrence in Bookends Server that could result in incorrect parsing of browser requests and a bug in handling of accented characters in SQLQuery searches.
Fixed a problem that could cause an error when syncing a Mellel document containing Bookends citations.
Update Amazon Online Search because of changes at Amazon that caused the spinning wheel to continue after finding and displaying less than 10 references.
Fixed a bug where the pdf would not be downloaded from the data detector if the reference didn't appear in the List View window (i.e. a group was selected or there was text in the live search box).
Improved error detection so that if you have designated a default attachments folder and it no longer exists, you will receive a intelligible error message when trying to move attachments to that folder.
Fixed problems in the creation of MLA citations that could cause error messages to be generated during a scan.
Fixed a number of problems with creating a new format when Bookends had been removed from the Bookends 10 folder.

New in Bookends 10.4 (Nov 5, 2008)

Improved MLA citations - Resolve ambiguous citations in a custom format by appending a letter to the year or adding the author's initials/ full name/short title until the citation is unique (the full title will be used if there is no short title). The latter is used in the MLA citation style.
Expanded format options - There is one group of settings for author and editor punctuation in a format (Name Punctuation tab), and the settings apply to all Types. Author and editor names can now have different settings.
Improved format definition window - There is one setting for author and editor punctuation in a format (Name Punctuation tab), and the settings apply to all Types. Author and editor names can now have different settings.
Redesign of the boolean online search interface - The boolean search fields and options appear in the main search window, not a drawer, and a number of improvements have been made in usability. Saved Amazon power searches from older versions of Bookends will not work with this version of Bookends and will need to be recreated.
Live feedback showing the groups to which a reference belongs - Hold down the Option key to highlight in yellow the groups (static and smart) to which the selected reference belongs. If more than one reference is selected, groups containing all will be highlighted. The reference or group list must have the focus when the Option key is pressed.
Autocomplete paper using ISI Web of Science - Requires access privilges and ip authentication.
Automatically move attachments to the Trash when a reference is deleted - The confirm deletion dialog has a checkbox "Move attachments to the Trash". Use this carefully, because it is possible to have more than one reference, perhaps in more than one database, attached to the same file. Note that this setting is ignored when you remove duplicates or delete references from the List View without the confirm dialog (that is, with Command-Delete).
Perform boolean NOT live searches - Exclude references containing given words by placing a dash (minus sign) before a word in the live search textbox. For example, "shakespeare -william" will find references containing the word "shakespeare" but not the word "william". The minus sign must precede each word that is to be excluded.
Edit references from a remote location using Bookends Server - You can edit references in Bookends databases that are available via Bookends Server. The syntax is detailed in the User Guide.
Smart group searches can be restricted to references that are or are not in any static group - References imported into Bookends by syncing with Papers, a Mellel document, or by drag and drop from another Bookends database are highlighted in the destination database.
After online search, select reference to import that are not in your database - After searching PubMed or Web of Science, right-click on the reference list and tell Bookends to select just the references that are not already in your database (the ones you have will be highlighted in yellow). This is handy if you want to quickly select and import the references you don't already have.
Display names in the list view as surname-only - Use the keyboard shortcut Option-Command-I in Term Lists to insert the selected terms into the corresponding field in the selected reference
Window -> Minimize Window works with any window in the Window menu
When attaching and autocompleting from Google Scholar based on the doi, Bookends will retrieve the most complete information available
Bug fixes:
Fixed an error that could arise when finding text in a reference.
Fixed a rare error in the Find dialog Spotlight search where nonmatching references were found.
Performing a Find from a Term List no longer generates an error.
Fixed a bug where an ampersand in an attached file's name might not show up in the Bookends attachment pop-up menu.
Word 2004 scans work properly when the insertion point is in a footnote when the scan is initiated (for users of older versions, they must replace the old Bookends Word X Template in Microsoft Office 2004 -> Startup -> Word with the new one). Fixed some rare cases when virtual groups could give incorrect results. Fixed a bug on Intel Macs where colored text settings were sometimes not saved correctly. Fixed an issue where an incomplete and invalid doi could be obtained from an attached pdf.

New in Bookends 10.3.4 (Oct 3, 2008)

New in Bookends 10.3.3 (Sep 15, 2008)

When you attach a pdf, Bookends will search it for a doi. If present, and the paper can be located on PubMed or Google Scholar, Bookends will offer to attach the pdf and then import the reference automatically. If no doi is found, Bookends will offer to attach the pdf to an new reference and then autocomplete it. This option opens a dialog that displays the pdf and provides several fields in which you can enter information from the pdf (author, title, year, etc.). A pop-up action menu in this dialog copies selected text from the attached pdf to the search fields, and in the case of authors or year will attempt to clean up the raw text to a form suitable for submission to the search engines. Bookends will use the information to search PubMed, Google Scholar, or JSTOR, and give you a list of the first 20 references that match. You can refine the search, if necessary, until you find the reference. Select it from the list, click on Import, and it will be downloaded to your database and the attachment associated with it. Note that you can also perform a Refs -> Autocomplete Paper on any reference already in your database that has a pdf or webarchive attachment.
Improvements in locating matching pdfs on the local hard drive
In the online search window the Import button will require one click if only one database is open and you are not reference surfing. Otherwise, the Import button will present a pop-up menu allowing you to select the database and/or whether to download and attach the current pdf/web page.
Drag and drop a group name to a compatible application (like Scrivener, DevonThink, and TextEdit) or use the Edit -> Copy Hypertext Link menu (which lets you copy the link as plain text as well). Clicking on that link the application will take you to the corresponding group in the open Bookends database. When using a hypertext link to find a reference or group in Bookends, the list view will be set to show all references if it's not already.
The logic for automatic removal has changed slightly. Now if two references have identical based on the match criteria, Bookends will keep the one with more attachments. If the number of attachments are the same, Bookends will keep the one with the longer Notes.
Help -> FAQ… takes you to the Sonny Software FAQ (Frequently Asked Questions) web page
In the format definition window, Show Example will use the information in the selected reference if the Types match (the reference Type and the Type selected in the format window). If they don't match, Bookends will use default reference information to create an example.
Improved conversion of smart groups from pre-10.3.2 databases to the new format. When outputting as BibTeX, en dashes are correctly converted to two hyphens (--). The modification date is now updated when a reference is altered by a Global Change operation. Fixed a problem with direct z39.50 searches failing to return accented characters correctly even when the text encoding was set correctly. Changed the escaped sequences for accented characters exports as BibTeX to match those used when importing BibTeX. Fixed a rare occurrence in which exporting references with a very large field that contained the super- or subscript character could cause a crash.

New in Bookends 10.3.2 (Aug 21, 2008)

New in Bookends 10.3.1 (Jul 25, 2008)

Web page reference metadata detectors: When you use Online Search and reference surf to a web site, Bookends will automatically detect the presence of embedded reference metadata. You will be alerted by the appearance of a green icon that, when clicked, will present a list of the references. Check the references you want to import (Bookends will offer to import the assocated pdfs, too, if it can find them).
Embed reference metadata in Bookends bibliographies: If enabled in Preferences, Bookends will add COinS (ContextObject in Span) reference information to bibliography files generated as HTML, or bibliographies that are delivered dynamically by Bookends Server. This means that anyone who accesses bibliographies on your web site or Bookends server will be able to see and download the references if they are using a browser that can detect COinS.
Automatic pdf download from Web of Science with one click: Check "Download pdf" in the Online Search window and use the Import pop-up menu or drag and drop the reference(s) onto a Bookends database window (access privileges required).
Open a reference's full text or pdf in the Bookends browser: In the Online Search window, double clicking on a reference will open the reference's full-text (if available) in the built-in Bookends browser (reference surfing). If you want to open it in your default browser, hold down the Shift key when double clicking. This works with PubMed, Web of Science, Google Scholar, JSTOR, Amazon, and arXiv.
Use File -> Open URL to access any web site in the Bookends browser: When the Online Search window is in front, File -> Open URL will use the Bookends browser to display the web site. Hold down the Shift Key to force the default browser to be used.
Improved importing from Google Scholar: When using Online Search with Google Scholar, Bookends will attempt to locate and import the most complete information Google Scholar offers. If no additional information can be found, Bookends will import the information available on the web page. Note that if you import by drag and drop (rather than with the Import pop-up menu) Bookends will import the information from the web page. The Google Scholar import filter is now obsolete.
The Online Search "download pdf" setting is remembered between launches
Import references from a text file by dropping the file onto the Bookends icon in the dock
Fixed a bug where the online search window would open when an automated PubMed search was performed.
Fixed Amazon.fr searches to ignore accented characters.
Em dashes in temporary citations are handled properly during a scan. Improvements in unscanning Word 2008 documents.
Fixed several problems with scanning of Pages documents, one which could cause the scan to abort with a error message.
Find/replace correctly finds the return character (�) if it's in the search string.

New in Bookends 10.3 (Jun 23, 2008)

New in Bookends 10.2.1 (May 26, 2008)

Reference surfing - Online Search contains a WebKit-based browser. After searching for references on web-capable sites (such as PubMed, Web of Science, JSTOR, arXiv, and Amazon) you can toggle the reference view from Text to Web. The built-in browser will take you to the reference on the web site, where you can navigate to the full text article or pdf (if available and you have access privileges). You can import the reference information and web pages/pdfs directly into Bookends with a click on the Import button. You can also attach the web pages/pdfs to an existing reference by drag and drop onto a Bookends database window (or save to disk by dropping on the Finder). Right-clicking on the web proxy icon brings up a contextual menu that lets you create a new empty reference and attach a web page/pdf, or attach the web page/pdf to a newly created Internet reference in which the title, URL, and date and year accessed are automatically entered. A URL field in the Online Search window lets you navigate to pages at any site you choose, where you can obtain pdfs or save the web pages. When the Online Search window is in front and the URL field is enabled, the File -> Go To URL menu will use the Online Search browser instead of your default browser. Note: the pdf download/import will not work if the Adobe or Schubert pdf plug-in are installed.
Live web pages/pdfs in the List View - You can copy text from pdfs attached to references, and hypertext links in attched web pages are live. A toggle in the Action pop-up menu lets you display pdfs with WebKit (links active, text selectable) or in the Bookends pdf viewer (links inactive, text not selectable).
Copy selected text from an attached pdf/web page to the reference - If you are using WebKit to display pdfs, select text and use the Action pop-up menu to "Copy selected text to" any field. If the field is authors or editors, Bookends will attempt to parse the names, assuming that they are surname last and separated by commas. Limitations: Bookends will remove non-letters from the names (e.g. superscripted numbers specifying footnotes), but will not remove superscripted letters. Also, pdfs often have spurious characters (often spaces) that you can't see but that are copied to the clipboard. Bookends will not remove these.
Attach a file to a new empty reference - If you have pdfs with no corresponding reference information, you can choose to have Bookends create a new empty reference and attach the pdf to it.
Searching JSTOR works again - This was broken by changes made in the JSTOR gateway
A BibTeX @collection reference will be imported as an Edited Book Type
Improved Change Case - Global Change -> Change Case -> Title Case will uppercase words that begin with punctuation (e.g. quote mark, bracket, etc.).
Color labels can be displayed and edited in the concise view pane
Book images obtained from Amazon will always be the highest quality available
Highlighting of a drag to a static group is much more obvious
Import article numbers from Web of Science - Some journals covered by the Web of Science use article numbers instead of page ranges. These are now displayed in the search window and imported to the Pages field in Bookends (using the AP tag). The doi for such articles, if present, will also be resolved properly.
Press Command-S to save an edited import filter
Don't Change Case can be applied to words containing hyphens - This means that words like X-ray can be added to the Don't Change Case list.
The virtual "issues" field can be used with the binding command in a format
The User16 field for Journal Articles is now used to store the PubMed Central ID number - This field has been renamed PMCID. The PubMed import filter has been modified to import the PubMed field containing the PMC into PMCID. If you have an older version of Bookends and renamed the User16 field for Journal Article, your label will be left intact.
Fixed several problems with Word 2008, including failure to remove an old bibliography when unscanning, unintended substitution of accented characters that followed a citation, and failure to recognize control characters like % or * or unicode characters immediately after the opening citation punctuation. Invoking the Word 2008 Scan and Unscan AppleScripts works when the cursor is placed in a footnote. Control-Command-1, 2, and 3 now corretly changes the label in the reference window rather than changing the tab selection. The items in an attached Mellel or Pages document bundle will not be listed in the attachment pop-up menu or in the list of subfolders in the attachment dialog.
Fixed a bug that prevented Bookends from importing an existing bibligraphy if the references were preceded by numbers. PDFs imported from a browser by drag and drop will be renamed correctly.
Fixed a problem in which a temporary citation without a closing citation delimiter (such as a curly bracket) would cause Bookends to abort a Pages scan.
Fixed a problem where scanning of some Pages documents could result in truncated citations.
Fixed an out of bounds error that could happen when opening a database created with a version of Bookends prior to 10.1.4 and selecting an unused Type of 11 or higher when creating a reference.
Fixed a problem where replicating a book as a book chapter would open the wrong reference window if the list view live search box has text in it.
Fixed a bug in which two citations containing a year and distinguishing letter would be incorrectly grouped when "Letters for repeated years" was checked in the format.
Fixed a bug in Online Search where the filter in the Bookends/Import Filters folder would be used even if there was a filter with the same name in the Custom Import Filters folder.
Fixed SRU search for the British Library (broken in the last update by changes made to accomodate JSTOR).

New in Bookends 10.2 (Mar 26, 2008)

New in Bookends 10.1.4 (Feb 20, 2008)

New in Bookends 10.1.3 (Jan 21, 2008)

New in Bookends 10.1.2 (Dec 7, 2007)

Sync databases: Synchronize Bookends databases across a network or the Internet. Sync can be configured to work for individuals who use Bookends in more than one location as well as groups that want to sync personal databases with a master copy. Sync will keep references (additions, deletions, and modifications) and groups up to date. Individual sync options will be shown before they are performed and can be denied on an ad hoc basis. Ancillary files, such as attachments, must be synchronized separately.
Enabled formats and filters are remembered after a Bookends update
The list of formats and filters you have enabled is stored in preferences and won't be reset when you upgrade Bookends.
Replicate As Book Chapter is enabled for Conference Proceedings
Duplicating a reference is faster when the unique id is in a numeric sequence
The date and time of duplication will be used as the date added for duplicated references
Improved show example for formats
If the example drawer in the format window is open, it will automatically update when you switch references in the List View.
More versatile bibliography sorting
You can specify that citations in a group can be sorted or not for both author-date and custom citation formats.
Improved Amazon searches
Bookends will remember the Amazon search category (Author, Title or Keywords, etc.) between launches. Amazon searches for 13 digit ISBNs work.
The ability to sort the physical order of references in the database has been removed
Bug fixes: Fixed a bug that prevented non-pdf images from being displayed in the list view. Updated the JSTOR import filter so that it downloads references properly. Fixed a bug in the info pane where pressing the return key in a field with a term list would enter two returns. Fixed a bug in the format examples where "Journal of Biological Chemistry" would be used for the full title even if a reference was selected. Double-clicking on a Bookends database with the extension .bdb will open it in Bookends regardless of the file type metadata. Retrieving a reference from PubMed when attaching a pdf works in Leopard. The punctuation after the last author that is ouput will be suppressed when using "et al.".

New in Bookends 10.1.1 (Nov 13, 2007)

Perform online searches of SRU-compatible libraries
New import filters have been added for JSTOR, British Library, and COPAC. Simple searches treat spaces like a boolean AND. To look for phrases, enclose them in quote marks. If "boolean search" is selected, the entries in one of the three fields are treated as if they are within quote marks.
Perform online searches of arXiv
arXiv (http://www.arXiv.org) is a premiere open access site for e-prints in physics, mathematics, computer ccience, quantitative biology, and statistics.
Smart attachment folders
You can attach folders to a reference. Bookends will list all the items in the attached folder and you can select any to view, reveal in the Finder, etc. Any files added to the folder in the Finder are automatically made attachments (and if you remove a file from the folder it is no longer treated as an attachment). Attachments in such a folder are one level deep (that is, a subfolder in the attached folder will be shown, but not any files in it). If you add/remove files from an attached folder, the list view will need to be refreshed to see the change (just click on the reference is sufficient for this).
Searches ignore diacritics
For example, searching for "Sch�tz" will find both "Sch�tz" and "Schutz". The exception is a Find search by character, in which case searching for "�" will not find "u". This applies to all new databases you create. You must Rebuild (Keep User Info or not) databases created with prior Bookends versions to have diactric-insensitive searches.
More versatile example display in the Format Manager
Clicking on the Example button will use the information (authors, title, etc.) from the reference window (if open) or the first selected reference in the List View (if open). If neither are open, default example information will be used. The example will update automatically when a different format is selected. Pressing Command-E when the formats manager is in front will toggle the example pane open and closed.
Replicate as Book Chapter works with Book as well as Edited Book
Sending attachments with e-mail works in Mac OS 10.5 (Leopard)
Hypertext links in the display pane in the Online Search window are live
Improved handling of non-Roman characters in Live Search
Improvements in Spotlight accuracy when matching references with local pdfs in Mac OS 10.5 (Leopard)
Bug fixes
Fixed a bug where sorting on the Added column in the List View could cause an SQL error. Fixed a nil object error when editing a reference with the List View closed. Bookends cleans up HTML entities from attachment names when importing XML from EndNote 9. Fixed a bug where the appearance of some pdfs would be incorect on PPC Macs. For the unmatched or ambiguous list after a scan, the type ahead function works even if an author's name begins with a unicode (accented) character. Fixed a bug in subject bibliographies where style runs in the first reference could be offset incorrectly. Edit -> Special Characters now works on Intel Macs. Fixed a bug that caused an error when importing references from Bookends 7.x that had fields with non-Roman characters and styled text.

New in Bookends 10.1 (Oct 16, 2007)

A highly configurable, interactive, and editable concise view: Two views, Summary and All, let you view the fields you want in the List View. These views are "live", meaning that you can click on the fields to edit them, assign ratings, go to linked URLs, and more.
Display up to seven columns in the List View
Redesigned Import Filter and Formats Manager windows: These windows have a unified look, with a list of filters/formats on the left and the settings on the right.
Text in a reference window tab indicated with an asterisk: In the reference window, an asterisk will be appended to the Notes or Keywords tab caption if that field contains text. This allows you to see if the field has information while you are viewing the main tab.
PDF orientation corrected if necessary: The List View display pane will always show a pdf in a readable orientation even if it was scanned in as a vertical image.
PDF viewer will skip damaged pages: It will write a message to the Console telling you which pages it couldn't read.
Improved DOI lookup from PDFs: Bookends works with more pdfs (for example those from PNAS and J Exp Med) to locate the citation information on PubMed when they are attached.
Automatic proxy server configuration: Bookends gets the HTTP proxy server and port information (if any) from System Preferences. If you are using an authenticating server, you still need to enter you user name (id) and password in Bookends Preferences, Internet tab.
Smarter Global Change: When doing a Global Change -> put after, if the word being inserted begins with a return character, the return will be suppressed if the receiving field is empty.
Include the list of static groups a reference belongs to in a formatted reference
Upload to Refbase using either XML or RIS output
Replicate as book chapter is enabled when the List View is in front
Bookends will offer to move format or filter you delete to the Trash
Improved BibTeX escaping of reserved and accented characters
References exported as XML retain full links to attachments: This means that if you import these into EndNote 9 or later the attached files will retain their links.
Bug fixes
Bookends will recognize attachments with the extension ".htm" as html files. Fixed a bug where Find PDF on the local drive would result in a list of possible hits but no pathnames visible. Fixed a bug where a new, not upgraded, Bookends Preference file would list duplicated column options for the List View. Fixed a bug where accented characters in the subject bibliography subject lists were not rendered properly. Fixed a bug where importing styled text from an EndNote 7 XML export file could cause an error on Intel Macs. Fixed a bug where a find/replace restricted to a field in the main tab could also finding matching text in a drawer field. Fixed a bug where the new name of a renamed SQL smart group wasn't shown. Fixed a bug where sorting by date added didn't work. Fixed a rare bug where a global change -> insert for a large number of references could corrupt the database. A cosmetic bug in which the List View fields could be drawn on top of one another after a rebuild was fixed.

New in Bookends 10.0.3 (Sep 12, 2007)

View attachments in a tab in the reference window: A pop-up menu at the bottom of the window lets you switch between multiple attachments. A contextual menu lets you manipulate the attachments.
More versatile display of attached files: Bookends can show the textual contents of attachments of many different file types: .doc (Microsoft Word), Mellel (XML), RTF, RTFD, Nisus Writer, and HTML. The display contains the main body of the text only (no text styles or images, and in the case of Mellel no note streams or footnotes). The Bookends Spotlight search will find text in these attachments if they are in the default attachments folder (or subfolders). Note that to find Mellel file attachments you must have installed the Mellel Spotlight plug-in. PDFs and images can be zoomed up to 300%.
Improved Remove Duplicates: If two duplicates are indistinguishable, the older one (the one with a lower sequential number) will be marked for deletion. The manual verification shows duplicate references side by side. Only fields that have information (in either reference) will be shown, and any fields that differ will be highlighted in red. Field names will be preceded by a clickable symbol. When clicked, a dialog containing that field from both references will allow you to copy/paste or drag and drop text from one to the other, so that you can merge the reference information into one reference and then mark the other for deletion. Navigation arrows let you move amongst duplicate pairs, or you can click on particular references to examine.
Compare references: If more than one reference is selected in the List View, you can use Refs -> Compare References to view the first two selected references side-by-side in a new window. Only fields that have information (in either reference) will be shown. In this window you can move between references using a stepper control or enter the numbers of the references you want to compare. You can mark/unmark the references in this window to add/remove them from the hits list, and assign ratings. Field names will be preceded by a clickable symbol. When clicked, a dialog containing that field from both references will allow you to copy/paste or drag and drop text from one to the other.
Show PubMed references you already have: When doing an online PubMed search, Bookends will highlight in yellow any retrieved references that are already in your database (determined by matching PMIDs). The database must be open. If more than one database is open, Bookends will examine the database nearest to the Online Search window.
Bookends will refuse to open a database located in the same folder as itself: This is done so that users won't inadvertently delete their databases when replacing the older with the newer Bookends Folder when upgrading Bookends.
Switch to a linked word processor with a menu command
Don't clean up consecutive spaces in formatted references: This format option tells Bookends to allow runs of spaces in a formatted reference. This is useful, for example, for formats like RIS that require two spaces between each field tag and the following hyphen.
Z39.50 Default connections assume returned text is encoded as UTF-8
Deleting a reference in the reference window has been simplified
You can delete references when a smart group is selected
The List View window title is the name of the database
Bug fixes: Fixed several cosmetic bugs where the width of the keywords or notes field in the main tab could be wider than the reference window, or the width of the keywords field in the second tab could be too narrow. Multiple OpenURL servers are now shown correctly in the list view contextual menu. You can now open attachments with long names via the display pane contextual menu. Fixed a problem where incorrect styled text data could result in a nil object error. Fixed a bug where creating a new reference when there was text in the live search box and one of the columns contained reference numbers would open a new reference window with text already entered from another reference. Edited styled text with unicode characters in the Notes field tab is saved correctly. Fixed a bug where a Mellel verify scan using a format with styled text to replace temporary citations would result in the RTF formatting commands being embedded in the citation object. Changes to the pdf zoom value using the contextual menu are now saved.