[Feature Request]: align git functionality

### What would you like to happen?

The git functionality currently is inconsistent between the file explorer and git commit perspectives.
It's ok to have some differences where that makes sensen and is documented, but the core git functionality should be aligned.

### Issue Priority

Priority: 2

### Issue Component

Component: Hop Gui

No files or tests are named. Start by comparing the file explorer and git commit perspectives in Hop Gui, inventory their current git operations, and check existing documentation for intentional differences. Done means the core git functionality is aligned, with any justified differences documented.

Written by the indexing model from the issue text.