tools: Use new github mupen64plus upstream repositories
tools: Use git remotes to generate diffs

The mupen64plus-ae repository already contains many objects from the
mupen64plus upstream repositories. Thus using these objects by using multiple
git remotes avoids downloading them again. Also using git to do the diff avoids
creating extra repositories with work-tree and makes the script path
independent inside the mupen64plus-ae repo.
tools: Use the mapping from diff-upstream in pull-upstream