docs: clarify gitignore management and backup handling

[yacosta738]

Updated website/docs/src/content/docs/reference/configuration.mdx to accurately reflect the .gitignore management logic implemented in src/config.rs:351-395.

Changes:

• Documented that .bak versions of literal destinations are automatically ignored.
• Clarified that module-map targets are expanded into individual entries.
• Explicitly stated that nested-glob destinations are skipped (due to being templates).
• Added documentation for the defensive .agents/skills/*.bak pattern.
• Updated the Scribe journal.

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PR created automatically by Jules for task 14330922111662938599 started by @yacosta738

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ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: ASSERTIVE

Plan: Pro

Run ID: 8382726d-9517-4b9f-bf52-cc9aac9c409b

📥 Commits

Reviewing files that changed from the base of the PR and between 0b6536f and 2a94a72.

📒 Files selected for processing (2)

• .agents/journal/scribe-journal.md
• website/docs/src/content/docs/reference/configuration.mdx

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📝 Walkthrough

Summary by CodeRabbit

• Documentation
  • Clarified .gitignore management documentation to precisely explain how AgentSync populates ignore patterns: literal symlink destination paths are added, backup patterns are created per destination with module expansions, template destinations are excluded from auto-ignoring due to their dynamic nature, and duplicates are automatically deduplicated.

Walkthrough

This PR documents the actual gitignore management behavior in AgentSync. A new journal entry identifies drift between the configuration reference and the real implementation logic, then the reference documentation is expanded to precisely clarify how .gitignore entries are generated: literal symlink destinations, per-destination .bak ignores with module-map expansion, exclusion of nested-glob template destinations, a defensive .agents/skills/*.bak pattern, and deduplication.

Changes

Gitignore Management Documentation

Layer / File(s)	Summary
Gitignore behavior clarification .agents/journal/scribe-journal.md, website/docs/src/content/docs/reference/configuration.mdx	Journal documents findings about the real .gitignore generation logic (module-map expansion, .bak handling, nested-glob exclusion). Configuration reference notes are expanded to specify literal symlink destinations, per-destination .bak ignores, defensive patterns, and deduplication of entries.

🎯 1 (Trivial) | ⏱️ ~3 minutes

🐰 A journal and docs aligned today,
Gitignore patterns laid out plain,
No more mysterious .bak dismay—
The truth is clear, again and again!

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title 'docs: clarify gitignore management and backup handling' directly and accurately summarizes the main changes, which focus on updating documentation to clarify .gitignore behavior and backup patterns.
Description check	✅ Passed	The description is directly related to the changeset, providing clear context about the documentation updates and their alignment with the actual implementation in src/config.rs.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch docs/gitignore-accuracy-14330922111662938599

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[sentry]

Codecov Report

✅ All modified and coverable lines are covered by tests.

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[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud