Add locked files and directory-only entries.

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>

manifest/manifest.go

@@ -15,6 +15,7 @@ type Entry struct {
 	Hash          string    `yaml:"hash,omitempty"`
 	PlaintextHash string    `yaml:"plaintext_hash,omitempty"`
 	Encrypted     bool      `yaml:"encrypted,omitempty"`
+	Locked        bool      `yaml:"locked,omitempty"`
 	Type          string    `yaml:"type"`
 	Mode          string    `yaml:"mode,omitempty"`
 	Target        string    `yaml:"target,omitempty"`