Refactor troubleshooting and usage documentation for clarity and organization

- Simplified the structure of TROUBLESHOOTING.md, consolidating sections and improving readability.
- Updated usage examples in USAGE.md to reflect direct invocation and integration patterns.
- Enhanced clarity on environment variables and their effects.
- Improved instructions for running Python scripts, using pip, and managing virtual environments.
- Added common patterns and troubleshooting tips for better user guidance.

Author: scc-tw