Checkpoint re-hashes all tracked files, stores changed blobs, and updates per-file timestamps only when content changes. Missing files are skipped gracefully. Status compares each tracked entry against the filesystem and reports ok/modified/missing. CLI: sgard checkpoint [-m message], sgard status. 4 new tests (changed file, unchanged file, missing file, status). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>