Change promptToStageAllAndRetry to run "git add -u"

**Is your feature request related to a problem? Please describe.**
When prompted with "You have not staged any files. Commit all files?" (promptToStageAllAndRetry), i expect the same behavior as "git commit -a", but instead it calls StageAll (git add -A).
Whereas "git commit -a" only stage files that have been modified and deleted, but not new files. Similar to "git add -u".

**Describe the solution you'd like**
Add another function like StageUpdated (git add -u), and keep using StageAll for other functions like handleStageAll where the behavior makes sense.

**Describe alternatives you've considered**
The StageAll function could maybe run "git add -u" all the time. But this again could be considered unwanted behavior by many.