Gitmodules update

This PR adds an additional optional parameter to the `merge` & `update-submodules` command allowing to redirect the submodules URL defined in .gitmodules to point at the authenticated Github user fork instead.

Concrete use case: meant to be used by all the daily jobs pushing  `merge/{dev_4_4/develop}/latest`. Thi change should allow the Jenkins Git plugin to clone `https://github.com/snoopycrimecop/openmicroscopy` and have all the submodules correctly pointing at snoopy's forks instead of the main repo's at checkout.