We've also decided against a seperate git repository for each plugin, due to the deployment complexity and dependencies between some of them.
It might be worth reconsidering this decision, as it sounds like it could be the root of your issues. As Richard says there are ways to manage deployment where each plugin is in its own repository, and it'll probably be simpler in the long run that trying to manage 30+ plugins alongside the Moodle codebase in a single git repo.