Document Git integration and the .bib backup extension change

[koppor]

Summary

This is a low-risk, documentation-only update (no code changes) generated by an automated monthly review that cross-references recent JabRef/jabref commits (roughly the last month, up to a719616) against this repository's content.

It fixes one factual/stale-doc issue and fills one significant documentation gap for a feature that shipped with no docs at all:

1. New: "Git Integration" page (en/collaborative-work/git-integration.md), linked from SUMMARY.md, collaborative-work/README.md, collaborative-work/sharedbibfile.md, and advanced/autosave.md.
   JabRef's File → Git menu (Commit / Pull / Push / "Share this library to GitHub") had no documentation anywhere in this repo. Motivated by:

   • jabref#16440 — "Add commit + push funcionality to git"
   • jabref#16722 — "Offer to initialize a Git repository on commit"
   • jabref#16723 — "Add SSH support for git remotes"
   • jabref#16718 — "Honor autosave setting on git commit"
   • jabref#16720 — fix: "File > Git > Commit" refused to commit without a reachable remote
   • CHANGELOG.md (Unreleased/Added): "Commit and push" button (#16339), semantic diff preview for Git commits (#16341)

   Exact dialog text, button labels, and the SSH-via-system-agent behavior were verified directly against the current jabgui source (GitCommitAction, GitCommitDialogView, SshAgentConnectorFactory, NetworkTab) rather than guessed, since none of it was previously documented. Note: the CHANGELOG also mentions "clipboard prefill" for the commit message field, but that was added and then removed again in-window (jabref#16463 → jabref#16773), so it is intentionally not documented as current behavior.

2. Fix: backup file extension changed from .bak to .bib.
   Updated en/advanced/autosave.md, en/advanced/debugging-your-library-file.md, and en/SUMMARY.md, which extensively described .bak as the automatic backup extension (including in the page title and a "how to .gitignore your .bak files" tip that is now actively misleading, since .bib-extension backups are normally written to JabRef's user data dir rather than next to the library). Motivated by:

   • jabref#16675 — "Use .bib extension for backup files" (fixes jabref#11454), confirmed via BackupFileType.java (BACKUP("Backup", "bib")) and BackupFileUtil.java.

3. New: jabkit pdf extract-references CLI command documented in en/jabkit.md, alongside a one-line mention of the pre-existing jabkit pdf update for context. Motivated by:

   • jabref#16186 — "Add jabkit pdf extract-references command", confirmed via PdfExtractReferences.java.

Not changed

Several other recent jabref changes were checked and found to already be adequately documented (e.g. OCR engine/language selection and Docling support in en/advanced/OCR.md are already fully up to date) or judged out of scope for a conservative pass (e.g. LibreOffice track-changes/partial-citation support, since the existing docs made no incorrect claim there to fix).

Test plan

• Doc-only change; no build/test required beyond GitBook rendering the new page and updated links correctly.
• Spot-check the new en/collaborative-work/git-integration.md page and the cross-links from SUMMARY.md / collaborative-work/README.md / sharedbibfile.md / autosave.md.

Given the low risk (docs only, each change backed by a linked jabref commit/PR), a quick review/merge would be appreciated.

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Generated by Claude Code

[qodo-free-for-open-source-projects]

PR Summary by Qodo

Document Git integration, .bib backups, and JabKit PDF extraction

📝 Documentation 🕐 10-20 Minutes

AI Description

• Document JabRef’s built-in Git synchronization, authentication, commit, and GitHub sharing
 workflows.
• Correct backup guidance for JabRef 6.0’s .bib extension and legacy .bak compatibility.
• Add JabKit PDF update and reference-extraction command usage.

Diagram

graph TD
  N["Docs navigation"] --> C["Sharing guides"] --> G["Git integration"]
  N --> B["Backup guide"] --> R["Recovery guide"]
  N --> J["JabKit guide"] --> P["PDF commands"]
  B --> G

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High-Level Assessment

The current approach is appropriate: it adds the missing Git guide within the existing collaborative-work hierarchy, corrects stale backup terminology at every affected entry point, and documents JabKit commands alongside existing CLI guidance. Scattering these details across release notes or external source links would be less discoverable and harder to maintain.

Files changed (7) +103 / -14

Documentation (7) +103 / -14

SUMMARY.mdExpose Git integration and rename backup documentation +2/-1

Expose Git integration and rename backup documentation

• Adds the Git Integration page to the sharing navigation. Updates the autosave page title to identify '.bib' as the current automatic-backup extension.

en/SUMMARY.md

autosave.mdCorrect automatic-backup extension and Git guidance +15/-9

Correct automatic-backup extension and Git guidance

• Documents JabRef 6.0’s transition from '.bak' to directly openable '.bib' backup files while preserving legacy compatibility details. Corrects storage and '.gitignore' guidance and links to the built-in Git integration guide.

en/advanced/autosave.md

debugging-your-library-file.mdUpdate backup recovery instructions for .bib files +2/-2

Update backup recovery instructions for .bib files

• Revises troubleshooting steps to locate current '.bib' backups while acknowledging legacy '.bak' files. Generalizes retention warnings so they remain valid across backup formats.

en/advanced/debugging-your-library-file.md

README.mdAdd Git integration to sharing documentation +5/-1

Add Git integration to sharing documentation

• Introduces built-in Git versioning as a supported sharing workflow and adds a content reference to the new guide.

en/collaborative-work/README.md

git-integration.mdDocument JabRef’s built-in Git workflows +64/-0

Document JabRef’s built-in Git workflows

• Adds a comprehensive guide covering commit, diff review, repository initialization, pull, push, HTTPS tokens, SSH-agent authentication, and GitHub sharing. It also explains save requirements, remote prerequisites, and the network-drive alternative.

en/collaborative-work/git-integration.md

sharedbibfile.mdCross-link shared libraries with built-in Git support +1/-1

Cross-link shared libraries with built-in Git support

• Expands the version-control recommendation with a link to JabRef’s Git integration and its commit, push, and pull capabilities.

en/collaborative-work/sharedbibfile.md

jabkit.mdDocument JabKit PDF reference extraction +14/-0

Document JabKit PDF reference extraction

• Adds usage guidance for 'jabkit pdf update' and 'jabkit pdf extract-references', including file and URL inputs, output examples, and extraction-mode selection.

en/jabkit.md

[qodo-free-for-open-source-projects]

Code Review by Qodo

🐞 Bugs (0) 📘 Rule violations (0) 📎 Requirement gaps (0) 🎨 UX issues (0) 🔗 Cross-repo conflicts (0) 📜 Skill insights (0)

1. Backup link targets old heading ✓ Resolved 🐞 Bug ≡ Correctness

Description

The debugging guide still links to the previous #what-are-.sav-.bak-and-.tmp-files fragment after
the target heading was renamed. The link therefore no longer navigates users to the backup-file
explanation.

Code

en/advanced/debugging-your-library-file.md[16]

+2. **Find and select all** [**backups files**](https://docs.jabref.org/advanced/autosave#what-are-.sav-.bak-and-.tmp-files) (the `.bib` files, or `.bak` files if they were written by a JabRef version before 6.0).

Evidence

The changed debugging step still references the old #what-are-.sav-.bak-and-.tmp-files fragment,
while the target heading now also contains .bib and the word backup, changing its generated
fragment identifier.

en/advanced/debugging-your-library-file.md[16-16]
en/advanced/autosave.md[26-26]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
The debugging guide's backup-files link uses the fragment generated by the old autosave heading, so it no longer navigates to the intended section after the heading rename.
## Issue Context
Update the fragment to match the renamed heading, preferably using a repository-relative link so future local checks can validate it.
## Fix Focus Areas
- en/advanced/debugging-your-library-file.md[16-16]
- en/advanced/autosave.md[26-26]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

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[koppor]

Good catch — fixed in 88f037a by reverting the "What are .sav, .bak and .tmp files?" heading text (the .bib clarification stays in the body instead), so the existing anchor link from debugging-your-library-file.md keeps working.

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Generated by Claude Code