Manual · Version 0.12.0

The Bibliofile
manual

Welcome to the Bibliofile manual. Bibliofile is a cross-platform, desktop bibliography manager for your .bib (BibTeX) research libraries — a fresh Electron rewrite of the classic BibDesk. It gives you a friendly three-pane window for browsing, searching, grouping, and editing references, a beautiful themed preview with rendered math and formatted citations, file attachments, Markdown notes, and the ability to pull new references from online databases — all while keeping your plain-text .bib file as the single source of truth.

This manual is organised as a sequence of chapters. If you're new, read them in order from Getting Started; otherwise jump straight to the topic you need.

Table of contents#

1

Getting Started

What the app is, opening a library, and a tour of the three-pane window (groups sidebar, publications table, detail pane), the header, the toolbar, light/dark themes, and what happens when the file changes on disk while you have it open.
2

Browsing & Searching

Reading and sorting the publications table, the configurable columns (the View → Columns menu and the Preferences manager, including the keyword/attachment/ Read icon columns), filtering with the live search box (quoted phrases and full-text PDF search — an index kept on disk, built only while the Full-text search preference is on, with a configurable page limit), Find Duplicates, and narrowing your view with the groups sidebar (Library, Static/Smart groups, and dynamic Author/Keyword categories).
3

Editing Entries

The standalone editor window (Publication → Edit Publication…, ⌘E / Ctrl+E, or a double-click), which is the full editor: changing fields (with field-value autocomplete), cite keys, and entry types; adding, duplicating, and deleting entries; Generate Cite Key (for one entry or a whole selection); Find & Replace across fields; the Copy clipboard commands and cite drag-out; Crossref inheritance; the @string macro editor; undo and redo; and explicit save.
4

Attachments

Attaching, opening (in your OS default apps), and removing files; the Links section for Url/Doi; AutoFile into a Papers folder; OCR Scanned PDFs… for image-only PDFs; how Bdsk-File-N links and relative paths work; keeping a library portable; and macOS BibDesk compatibility.
5

Notes & Abstracts

Writing abstracts and per-entry notes in Markdown (with math), plus notes-only extras: [[citeKey]] cross-references between entries and inline iframe embeds; and the standalone annotation editor window (right-click → Edit Annotation…) with auto-save.
6

Preview & Citations

The typeset preview card (title, venue, chips, keyword tags, rendered abstract) and the live, formatted CSL citation block (APA / Vancouver / Harvard, or any CSL style you install), in light or dark mode; plus the Copy Citation and Copy as BibTeX clipboard commands.
7

Importing & Exporting

Getting references in (pasting BibTeX — including Publication → New Publications from Clipboard, ⌥⌘L / Alt+Ctrl+L — drag-and-drop, and File → Import for BibTeX, RIS, and EndNote files) and out (File → Export to BibTeX / RIS / CSV / a styled HTML bibliography / RTF, plus your own export templates); and File → Clone Bibliography…, which copies a library and its attached files to a new .bib.
8

Online Search

Searching the six built-in sources (CrossRef, OpenAlex, PubMed, arXiv, plus DOI and ISBN lookup) from inside the app and importing results as new entries: the workflow, the fields each source captures, and troubleshooting.
9

Shortcuts & Reference

The complete menu-bar, keyboard-shortcut, and mouse-action reference, the file format and on-save normalisations, where each kind of data is stored, a special-field reference, citations, the x-bibdesk:// automation URLs, current limitations, a glossary, and general troubleshooting.
10

Configurable Panels

Resizing, hiding, and switching the panels: the detail pane's content dropdown plus the 🤖 Claude toggle, the bottom panel's Annotation · Tabbed · LaTeX Preview modes (the Tabbed view's Annotation/Abstract/Attachment-thumbnail tabs, and true BibTeX/.bst typesetting of the selection), the View → Side/Bottom Panel shortcuts, the multi-select view, the floating batch-edit bar, and the row context menu.
11

Customizing Panels & Outputs

Designing your own panel and output templates with Handlebars: the context fields, helpers, live widgets, interactive hooks, and worked examples.
12

Scripting with JavaScript

Automate your library with JavaScript: the Script Console, the bibliofile API, saved scripts, file and network access, change hooks, and worked examples.

Conventions used in this manual#

  • Key notation. Keyboard shortcuts are shown for both platforms, macOS first: ⌘O / Ctrl+O. ⌘ is the macOS Command key; on Windows and Linux the equivalent is Ctrl. ⇧ is Shift, ⌥ is Option/Alt — so ⇧⌘I / Shift+Ctrl+I is Shift+Command+I (macOS) or Shift+Ctrl+I (Windows/Linux), and ⌥⌘F / Alt+Ctrl+F is Option+Command+F or Alt+Ctrl+F. Enter is the Return/Enter key.

  • Menu paths are written with arrows: File → Import → From File… means the From File… item in the Import submenu of the File menu.

  • Interface labels — buttons, menus, fields, and on-screen text — are in bold: the 🌐 Online… button, the File → Save command, the Author field. Where a button carries an icon, the manual writes that icon as the nearest emoji: the 🌐 Online… and 🤖 Claude buttons show a globe and a robot in the app itself.

  • Literal text you type or that appears in your file — cite keys, field values, file names, BibTeX — is in a monospace font, for example the cite key einstein1935 or the field Bdsk-File-1.

  • Callouts highlight things worth pausing on:

    Note: Extra context or a clarification.

    Tip: A shortcut, or a faster way to do something.

    Warning: Something that can cost you data or time if you ignore it.

  • Cross-references appear as links, like Getting Started, and point to the relevant chapter.

Tip: Throughout the app and this manual, remember the golden rule: your .bib file is the single source of truth, and edits are not written until you save (⌘S / Ctrl+S). There is no autosave by default (you can turn one on in Preferences). And if the file changed on disk after you opened it, saving stops to ask — Overwrite, Reload from Disk, or Cancel — so an edit made outside the app is never silently replaced (see Getting Started).

Getting started quickly#

  1. Choose File → Open… (⌘O / Ctrl+O) and pick a .bib file.
  2. Click a row to inspect an entry; click a column header to sort; type in the search box to filter.
  3. Double-click a row (or press ⌘E / Ctrl+E) to open its editor window and change fields, then press ⌘S / Ctrl+S to save.

For the full tour, start with Getting Started.