Locked files (--lock): repo-authoritative entries. Checkpoint skips them (preserves repo version). Status reports "drifted" instead of "modified". Restore always overwrites if hash differs, no prompt. Use case: system-managed files the OS overwrites. Directory-only entries (--dir): track directory itself without recursing. Restore ensures directory exists with correct permissions. Use case: directories that must exist but contents are managed elsewhere. Add refactored to use AddOptions struct (Encrypt, Lock, DirOnly) instead of variadic bools. Proto: ManifestEntry gains locked field. convert.go updated. 7 new tests. ARCHITECTURE.md and README.md updated. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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