core: make patch tool more reliable and consistent with other editing tools

The patch tool now works seamlessly alongside other file editing tools with improved
error handling and a more intuitive permission system. Users will experience:

- More reliable patch application with better error messages
- Consistent permission prompts that match other editing tools
- Smoother integration when applying complex multi-file changes
- Better feedback on what changes are being made before applying patches

This refactoring leverages the robust patch parsing engine while making the tool
feel native to the opencode workflow, reducing friction when making bulk changes
to your codebase.