multiple VCS repositories in the same project

How does one manage commits for different repositories in the same project?
I have a Project where the whole project is a git repositories, and in one of the gitignored directories there is a subversion project, registered with PhpStorm.

But when I choose "commit" in the editor it'll popup a window asking me to commit all the modified files at the same time, with the same commit message. And the window says I'm commiting to the git repository, not to the subversion one...

Is there a way to manage this scenario and have a finer control of commists?

I would have expected that PhpStorm would have kept different changelists for each of the VCS roots automatically, and somehow ask me which one I'd be commiting on each commit....

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