* Fix deletion of committed files excluded in .gitignore, show branch info
* Add clickable branch links and support for remote branch/PR checkout
- Branch names in UI are now clickable and link to GitHub
- Added --remote-branch option to checkout remote branches
- Added --pr option to checkout specific PRs by number
- Fixed shadow repo sync to preserve git-tracked files regardless of gitignore
- Updated documentation with shadow repo sync principles
* Save work before checking out remote branch
* Checkpoint
* Checkpoint
* Checkpoint