fix(extraction): index nested non-submodule git repos (#193)#217
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`codegraph init -i` from a git super-repo containing independent nested git repositories (not submodules) reported "No files found to index": git ls-files reports an embedded repo only as an opaque `subdir/` entry and never lists its files. Detect embedded repos via that trailing-slash signal and recurse `git ls-files` into each, indexing tracked + untracked source and honoring each repo's own .gitignore. Reported by @timxx. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Fixes #193 —
codegraph init -ireported "No files found to index" when run from a top-level workspace that is itself a git repo and contains nested independent git repositories (separate clones, not submodules — a common CMake "super-repo" layout). Indexing each sub-repo individually worked; indexing from the workspace root did not.Root cause
git ls-filestreats an embedded (nested, non-submodule) repo as opaque: tracked output skips it, and untracked output reports it only as asubdir/directory entry, never its files. The filtered result was empty, so the git fast-path ingetGitVisibleFilesreturned zero source files.Fix
Extracted a recursive
collectGitFiles()that detects embedded repos via git's trailing-slash signal (a normal untracked dir expands to its files; only an embedded repo shows assubdir/), guards with a.gitexistence check, and re-runsgit ls-filesinside each — indexing tracked + untracked source with correct prefixed paths, honoring each repo's own.gitignore. Composes with the existing--recurse-submoduleshandling (#147).Per the documented "respect
.gitignoreat all levels" principle, a sub-repo that the parent repo's.gitignoreexcludes is intentionally still skipped.Tests
Nested non-submodule git reposblock: embedded repos discovered from a git super-repo (committed and untracked source), and per-repo.gitignorerespected.codegraph init -iagainst the issue's exact layout now indexes the nested files.Reported by @timxx.
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