First add the repo you want to merge in
git remote add other /path/to/other
Next, fetch the changes from that remote.
git fetch other
Now do a normal merge
git merge --no-ff other/master
Or a subtree merge? (Not tested)
git subtree merge --prefix=other other develop
When merging .gitmodules, it's easier to deal with if they're sorted. See git-config-sort.py.