refactor: enhance error handling with structured logging across multiple modules

- Updated various modules including cli.py, run_agent.py, gateway, and tools to replace silent exception handling with structured logging.
- Improved error messages to provide more context, aiding in debugging and monitoring.
- Ensured consistent logging practices throughout the codebase, enhancing traceability and maintainability.

tools/skills_sync.py

@@ -13,11 +13,14 @@ newline-delimited list of skill names that have been offered to the user.
 """
 
 import json
+import logging
 import os
 import shutil
 from pathlib import Path
 from typing import List, Tuple
 
+logger = logging.getLogger(__name__)
+
 
 HERMES_HOME = Path(os.getenv("HERMES_HOME", Path.home() / ".hermes"))
 SKILLS_DIR = HERMES_HOME / "skills"
@@ -131,8 +134,8 @@ def sync_skills(quiet: bool = False) -> dict:
             try:
                 dest_desc.parent.mkdir(parents=True, exist_ok=True)
                 shutil.copy2(desc_md, dest_desc)
-            except (OSError, IOError):
-                pass
+            except (OSError, IOError) as e:
+                logger.debug("Could not copy %s: %s", desc_md, e)
 
     _write_manifest(manifest)