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.

hermes_cli/main.py

@@ -39,9 +39,13 @@ env_path = PROJECT_ROOT / '.env'
 if env_path.exists():
     load_dotenv(dotenv_path=env_path)
 
+import logging
+
 from hermes_cli import __version__
 from hermes_constants import OPENROUTER_BASE_URL
 
+logger = logging.getLogger(__name__)
+
 
 def cmd_chat(args):
     """Run interactive chat CLI."""
@@ -512,8 +516,8 @@ def cmd_update(args):
                 print(f"  + {len(result['copied'])} new skill(s): {', '.join(result['copied'])}")
             else:
                 print("  ✓ Skills are up to date")
-        except Exception:
-            pass
+        except Exception as e:
+            logger.debug("Skills sync during update failed: %s", e)
         
         # Check for config migrations
         print()