Had the same problem just the moment ago and ended up deleting the submodule reference (as outlined in this article) and recreating it where i wanted it to go.
To follow your example of moving submodule jquery into repos/jquery
- Delete the (typically three lines) submodule reference from
.gitmodules.
- Check
.git/config for references to the submodule and remove them, if existent
- do
git rm --cached jquery to cut the submodule reference out of the repository
- remove the old submodule folder
- recreate you submodule reference (as you possibly did before) with
git submodule add git://github.com/jquery/jquery.git repos/jquery
In case your submodule was set to specific tag, respectively commit (which you'll surely have in a stable project) you will have set it again.
Due to this complex process i am strongly hoping there is (or will be, at least on the git roadmap) a more straightforward way of achieving this. If not, surely some scripts could be fumbled together to do this quicker...