feat: index files inside git submodules

[andreinknv]

Summary

git 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 #86.

• 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.
• 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.
• 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).

Opt-out

Submodule 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.

Behavior on failure

• Parent-repo git status failure → falls back to the full filesystem scan (preserves the prior null contract).
• Submodule-internal git status / ls-files failure → silently absorbed (e.g. uninitialized or partially fetched submodules).

Files changed

File	Change
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
src/types.ts	Add indexSubmodules?: boolean to CodeGraphConfig, default true in DEFAULT_CONFIG
__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

Test plan

• npm test (serialized): 385/385 pass (was 379, added 6 — 5 submodule + 1 internal helper test indirectly)
• npx tsc --noEmit clean
• npm run build clean
• Reviewer to spot-check on a real repo with multiple submodules

🤖 Generated with Claude Code

[giovannidoni]

Stumbled upon this issue - cool to see there is a pr opened for it!