fix: restore all removed bundled skills + fix skills sync system

- Restored 21 skills removed in commits 757d012 and 740dd92:
  accelerate, audiocraft, code-review, faiss, flash-attention, gguf,
  grpo-rl-training, guidance, llava, nemo-curator, obliteratus, peft,
  pytorch-fsdp, pytorch-lightning, simpo, slime, stable-diffusion,
  tensorrt-llm, torchtitan, trl-fine-tuning, whisper

- Rewrote sync_skills() with proper update semantics:
  * New skills (not in manifest): copied to user dir
  * Existing skills (in manifest + on disk): updated via hash comparison
  * User-deleted skills (in manifest, not on disk): respected, not re-added
  * Stale manifest entries (removed from bundled): cleaned from manifest

- Added sync_skills() to CLI startup (cmd_chat) and gateway startup
  (start_gateway) — previously only ran during 'hermes update'

- Updated cmd_update output to show new/updated/cleaned counts

- Rewrote tests: 20 tests covering manifest CRUD, dir hashing, fresh
  install, user deletion respect, update detection, stale cleanup, and
  name collision handling

75 bundled skills total. 2002 tests pass.

gateway/run.py

@@ -2410,6 +2410,13 @@ async def start_gateway(config: Optional[GatewayConfig] = None) -> bool:
         )
         return False
 
+    # Sync bundled skills on gateway start (fast -- skips unchanged)
+    try:
+        from tools.skills_sync import sync_skills
+        sync_skills(quiet=True)
+    except Exception:
+        pass
+
     # Configure rotating file log so gateway output is persisted for debugging
     log_dir = _hermes_home / 'logs'
     log_dir.mkdir(parents=True, exist_ok=True)