PHPStorm supports the use of multiple version control systems for different directories. If you setup all VCS roots correctly in the VCS settings dialog, it will transparently track, commit, diff etc. changes in an unified manner, picking the appropriate VCS and repo automatically.
However, setting up all those roots can be tedious – especially when you install
dev -variants for a lot of libraries with composer. So, without further ado, here's a quick'n'dirty PHP script that will create the necessary XML configuration file for you.
Simply run it from your projects base directory as
phpstorm-init-vcs-roots > .idea/vcs.xml .