Maintain Selected Changes During Update & Restart

**Please describe the problem you think should be solved**
Currently doing an update & restart will lose any selected changes and revert back to all changes being selected. This discourages me from doing timely updates (and leaves the banner coming up to annoy me) as I often use selected changes as an 'in-progress' tracker for my next commit, as commits aren't always in chronological order if I find a small change I can make an atomic commit, I'll go ahead and do that before I forget. As such I'll avoid doing an update during this time lest I lose these subset of changes. I could do a commit and then undo it after the restart, but this feels hackish, and if there's changes selected on multiple repositories is a pin.

I've limited the scope of the title to just update & restart rather than maintaining selected changes between closing and starting the program. That seems like a trickier thing to handle since the files may have changed while the program was closed, so the cached selected changes no longer apply. The update & restart seems like a small enough window where it's unlikely anything will change during that time.

Start by tracing the Update & Restart flow described in the issue and how selected changes are represented for multiple repositories. Confirm where the restart boundary occurs and verify that the selected subset remains selected afterward without requiring changes to persist across a full application close.

Written by the indexing model from the issue text.