Adjust the git submodule paths for Forking potential. (#3)
We use relative paths for many of the RosettaCommons submodules, to
allow for https/ssh flexibility. However, for the open repository if
someone were working off a fork, they wouldn't be able to get the
submodules unless they also forked the submodule.
To fix that, we can be explicit about the RosettaCommons organization in
the submodule URL.
This PR also updates the tools repo and (most of) the benchmark tests to use the main branch instead of the master branch.