feat(tools): add skills sync manifest with user-edit preservation

[lml2468]

Fixes #55

Summary

• Add SkillManifest and ManifestEntry data structures for tracking synced skill state including content hashes, source, install time, and user-modification flag.
• Add LoadManifest / SaveManifest with atomic writes (temp file + os.Rename) at ~/.hermes/skills/.manifest.json.
• Add IsUserModified for user-edit detection by comparing current file hash against the manifest hash; user-modified skills are never overwritten during sync.
• Integrate manifest into SyncBuiltinSkills: load manifest, check user edits, skip modified files, update hashes, save manifest.
• Add SyncFromHub stub for future GitHub-based skill index fetching.
• Add comprehensive tests: manifest round-trip, atomic write, user-edit detection, sync integration, hub stub.

Test plan

• go test ./... -count=1 passes (all packages)
• Manifest round-trip: save and reload preserves all fields
• Atomic write: no temp files left behind, valid JSON on disk
• User-edit detection: unmodified files sync normally, modified files are skipped
• Sync integration: manifest is created on first sync, hashes update on re-sync
• SyncFromHub stub returns nil without error