[markshust]

Summary

Fixes two gaps in marko/codeindexer that made marko-lsp/marko-mcp report false marko.config.unknown_key diagnostics.

Composer changes now invalidate the index. IndexCache::build() persists a composerState fingerprint (path, mtime and size of vendor/composer/installed.json, falling back to composer.lock) in the cache payload. isStale() compares it to the current value, so composer require, update and remove mark the index stale and the next read rebuilds it. Vendor files are still not walked one by one, so the check costs a single stat. A payload without the new key, from an older version, counts as stale and rebuilds once.

The project-root config/ is indexed. The new ConfigScanner::scanDirectory() (which scan() now delegates to) scans <root>/config/*.php during build(). Those keys are recorded under the module name project (IndexCache::ROOT_CONFIG_MODULE). <root>/config is part of both the mtime walk and the tracked-path set, so edits, additions and deletions there also mark the index stale.

Also:

• isStale() calls clearstatcache() first, so long-lived servers see changes other processes made to the files they stat.
• Removed the code comments and docs that said vendor is excluded (codeindexer.md, troubleshooting.md, verification-checklist.md).

packages/devai is unchanged. Its CLAUDE.md promise that the index rebuilds itself is now accurate.

Tests

New packages/codeindexer/tests/Unit/Cache/IndexCacheComposerStateTest.php uses the real walker and scanners:

1. A vendor package added and installed.json touched: the index is stale, and getConfigKeys() on the same instance contains new.*.
2. A vendor package removed: the index is stale and its keys are gone.
3. Falls back to composer.lock when installed.json is absent.
4. A fresh process does not load the stale cache after a Composer change.
5. <root>/config/app_only.php is indexed. Editing it or adding a new root config file marks the index stale.

Closes #649

🤖 Generated with Claude Code

https://claude.ai/code/session_017KaHtYgss6ELkNd1fkcNyX