index_repository silently ignores git global core.excludesFile — globally-excluded files are indexed

[everclear077]

Version

latest (main, as of 2026-06-18)

Platform

macOS (Apple Silicon)

Install channel

GitHub release archive / install.sh / install.ps1

Binary variant

standard

What happened, and what did you expect?

Actual behavior: When indexing a repository, the tool reads only per-directory .gitignore files committed inside the repo. The global exclude file referenced by git config core.excludesFile (e.g. ~/.gitignore_global on macOS/Linux, %USERPROFILE%\.gitignore_global on Windows) is silently ignored.

Files the user has told git to exclude globally — .DS_Store, Thumbs.db, .idea/, *.pyc, __pycache__/, IDE config directories — are fully indexed and appear in the knowledge graph.

Expected behavior: The indexer should honour all three layers of git's --exclude-standard exclude chain:

1. Per-directory .gitignore files ✓ (works today)
2. $GIT_DIR/info/exclude (tracked separately in index_repository ignores .git/info/exclude (only .gitignore honored) → indexes excluded worktrees → OOM #489)
3. Global core.excludesFile (this issue — currently unhandled)

git ls-files --exclude-standard already reads all three layers; the indexer's tree walk should match that behaviour.

Reproduction

1. Configure a global gitignore and add a pattern:

   git config --global core.excludesFile ~/.gitignore_global
   echo "*.pyc" >> ~/.gitignore_global
   

2. Create a minimal test repo with a .pyc file not listed in any in-repo .gitignore:

   mkdir /tmp/testrepo && cd /tmp/testrepo && git init
   touch foo.py foo.pyc
   

3. Index the repo:
   codebase-memory-mcp index_repository '{"project":"/tmp/testrepo"}'

4. Query for the excluded file:
   codebase-memory-mcp cli search_graph '{"project":"/tmp/testrepo","name_pattern":"foo.pyc"}'

Expected: no results — foo.pyc should be excluded by the global gitignore.
Actual: foo.pyc appears as a graph node — core.excludesFile was not consulted.

Cross-check: git -C /tmp/testrepo ls-files --exclude-standard --others returns nothing for foo.pyc, confirming git itself respects the global exclude file at all three layers.

Logs

Project scale (if relevant)

No response

Confirmations

• I searched existing issues and this is not a duplicate.
• My reproduction uses shareable code (a dummy snippet or a public OSS repository), not proprietary code.

[DeusData]

Thank you for the clear report, @everclear077 🙏 You're right, and it's cleanly separated from #489. Discovery reads in repo .gitignore and .cbmignore today, but not the other two layers of git's exclude chain: .git/info/exclude (that's #489, with a fix in flight as #493) and the global core.excludesFile (this one).

The global layer needs us to resolve git config core.excludesFile, including the XDG ~/.config/git/ignore default, and load it as a repo root ignore source. We'll track this as the third layer on top of #493. Thanks for cross checking against git ls-files!