Use git to merge local ~/.* changes with upstream changes.

Instead of blowing changes away with `rsync`.

It’s annoying when trying out changes to have to edit files in `~/dotfiles`, then run `bootstrap.sh` after each change.

Perhaps there is a way to keep the .git directory in `~/dotfiles` but use the files in `~`?

Start by reading bootstrap.sh and tracing how rsync currently updates files from ~/dotfiles into ~. Investigate whether Git can preserve the .git directory in ~/dotfiles while using files in ~, and define a workflow that keeps local edits while incorporating upstream changes; done means local changes are not overwritten during bootstrap.

Written by the indexing model from the issue text.