feat: index files inside git submodules

[mschreib28]

Summary\n\ngit ls-files (used for both the initial scan and incremental sync) doesn't enter submodules — they appear as gitlink entries with their contents invisible. Both file-discovery paths now recurse into active submodules. Closes colbymchenry#86.\n\n- getGitVisibleFiles (full index) enumerates active submodules via git submodule foreach --recursive --quiet and runs git ls-files -co --exclude-standard inside each, prefixing paths so files are reported relative to the parent root.\n- getGitChangedFiles (sync) was refactored to share its status-parsing logic between the parent repo and each submodule. Submodule directory entries the parent's status emits (e.g. m vendor/sub when the pointer moved) are filtered out so we don't try to read a directory as a file.\n- Status output paths are now C-style-unquoted before use, so submodule directories containing spaces or non-ASCII bytes are handled correctly (also fixes an existing latent bug for non-submodule paths with spaces).\n\n## Opt-out\n\nSubmodule indexing is on by default. For repos with very large vendor submodules, set indexSubmodules: false in CodeGraphConfig to skip them. Path-based excludes (e.g. '**/vendor/**') also still work.\n\n## Behavior on failure\n\n- Parent-repo git status failure → falls back to the full filesystem scan (preserves the prior null contract).\n- Submodule-internal git status / ls-files failure → silently absorbed (e.g. uninitialized or partially fetched submodules).\n\n## Files changed\n\n| File | Change |\n|---|---|\n| src/extraction/index.ts | Add getGitSubmodules / getSubmoduleFiles; recurse into submodules from getGitVisibleFiles; refactor getGitChangedFiles to share readGitStatus; add unquoteGitPath for C-style-quoted porcelain paths |\n| src/types.ts | Add indexSubmodules?: boolean to CodeGraphConfig, default true in DEFAULT_CONFIG |\n| __tests__/sync.test.ts | 5 new tests: indexAll picks up submodule contents, sync detects modifications inside a submodule, sync detects new untracked files inside a submodule, missing submodule directory doesn't break the scan, indexSubmodules: false skips submodule contents |\n\n## Test plan\n\n- [x] npm test (serialized): 385/385 pass (was 379, added 6 — 5 submodule + 1 internal helper test indirectly)\n- [x] npx tsc --noEmit clean\n- [x] npm run build clean\n- [ ] Reviewer to spot-check on a real repo with multiple submodules\n\n🤖 Generated with Claude Code\n

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Copied from colbymchenry/codegraph#93