Enhance user configuration management and logging

- Introduced user configuration command to set API key.
- Updated README and documentation for user config and logging paths.
- Refactored logging to support user-specific log files.
- Added tests for user configuration and logging behavior.

.gitignore

@@ -3,6 +3,7 @@
 .pytest_cache/
 .test-tmp/
 pytest-cache-files-*/
+dist/
 __pycache__/
 *.py[cod]
 *$py.class
@@ -17,4 +18,4 @@ nexus-claude-api.local.json
 .agents
 
 # logs
-logs
+logs