fix(scan): honor .codegraphignore on the git fast path

[mschreib28]

Summary\n\nThe .codegraphignore marker (per-directory opt-out from indexing) was respected by scanDirectoryWalk (the filesystem-walk fallback) but silently ignored by getGitVisibleFiles (the git fast path) and getGitChangedFiles (sync's git path). Same project gave different file sets depending on whether .git existed — typically the marker "worked" only on non-git scratch projects and was a no-op everywhere else, the opposite of how most users encounter it.\n\n## What changed\n\nTwo helpers in src/extraction/index.ts:\n\n- findCodegraphIgnoredDirs(rootDir, files) — walks parent directories of the given file list, returns the set of dirs that contain a .codegraphignore marker. Walks once per unique parent directory with an early-out on shared ancestors.\n- isUnderCodegraphIgnoredDir(filePath, ignoredDirs) — true if filePath lives under any of those dirs.\n\nApplied at three sites:\n- scanDirectory and scanDirectoryAsync — between the git file list and the include-pattern filter\n- getGitChangedFiles — refactored to a two-pass collect-then-bucketize so the ignored-dir set is built once from the candidate paths\n\nThe marker file itself does not need to be tracked by git — fs.existsSync catches it whether it was committed or added as a local override.\n\n## Files changed\n\n| File | Change |\n|---|---|\n| src/extraction/index.ts | Add findCodegraphIgnoredDirs + isUnderCodegraphIgnoredDir; apply in scanDirectory, scanDirectoryAsync, getGitChangedFiles |\n| __tests__/codegraphignore.test.ts | 6 regression tests |\n\n## Test coverage\n\n- scanDirectory honors marker in a subdir on the git fast path\n- Marker at project root excludes everything\n- Marker in one subdir does not affect siblings\n- Marker added as local override (untracked) is still respected\n- Non-git fallback parity (sanity, pre-existing behavior unchanged)\n- Sync (getGitChangedFiles) ignores changes inside marker dirs\n\n## Known limitation (pre-existing, out of scope)\n\nIf a .codegraphignore marker is added after files in that directory have already been indexed, the next sync via the git fast path won't proactively delete those stale rows — git status doesn't report unchanged files. The next full indexAll (or a sync that falls into the filesystem-walk path) will clean them up. This is an existing characteristic of the git fast path; documenting here for transparency rather than fixing in this PR.\n\n## Test plan\n\n- [x] npm test: 386/386 pass on macOS (one pre-existing fs.watch flake under parallel load, passes in isolation)\n- [x] npx tsc --noEmit clean\n- [x] Independent reviewer pass before pushing — verdict APPROVE; addressed two info-level cleanups (JSDoc accuracy, removed dead try/catch around fs.existsSync which never throws)\n\n🤖 Generated with Claude Code\n

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Copied from colbymchenry/codegraph#103