Rework linters and fix submodule linter

Previously these expected their first argument to be the path to a .git directory since they were run from bare repositories (on the gitolite server). However, these are no longer run on the upstream bare repositories but instead are run on full working directories. Consequently the linters now take the path to the working directory (although a .git directory will also work).

We also adjust the submodule linter to look at the branches of the working directory instead of the bare gitolite reposotories.