The structures of my Git repositories look like this:
A-B-C-D-E-F # master branch in separate repo1
A-B-C-D-E-G-H # master branch in separate repo2
You can treat another git repository on the same filesystem as a remote repo.
In the first, do the following:
git remote add /path/to/other/repo/.git
git fetch
git branch /master #optional
Now they're both branches in a single repository. You can switch between them with git checkout, merge with git merge, etc.