Add directory ignore functionality and fix syntax highlighting

- Add --ignore flag to exclude specific directories from processing
- Add -y flag to skip confirmation prompts
- Show directory file counts when warning about large repositories
- Fix syntax highlighting by removing CSS interference and using JavaScript highlighting for Solidity
- Categorize themes by light/dark backgrounds in documentation
- Update README with new command line options and examples

These improvements make the tool more flexible for handling large repositories with better user control and working syntax highlighting themes.