Commit git from a sub project

I am developing a symfony app using separate bundles that I also develop. That means, that I have a root "App" project, and several bundle projects that are loaded via composer.

To make development easy, all of the bundles as well as the root app are separate git repositories on my server.

Composer loads bundles into the "vendor" folder - which is ignored in the root app project as to not clutter the git repository.

Now, it gets interesting when developing this using PHPStorm. I spend most of my time developing the bundles (inside the vendor-folder). I solved this by adding the bundle projects as favorites, as to make navigating between them easier (they are also co-dependend to a degree).

The problem is committing these changes. PHPStorm seems to only "see" the root git repository and not the sub projects inside the "vendor" folder. This makes it impossible to commit changes from one of the bundle projects through PHPStorm.

If I navigate to the folder in my explorer, I can commit just fine (as it should be, as it's just another git repo on my system).

I googled and found this site which seemingly explains the exact issue I have: http://www.jetbrains.com/phpstorm/webhelp/git-branches-in-multirooted-projects.html

Problem is: That doesn't work for me. When I right-click one of the bundle projects from my favorites, and go to "Commit directory", PHPStorm tellts me there are no changes. If I do the same via the explorer (using TortoiseGit), I see all my local changes just fine.

Am I doing something wrong? Or is the page I found not really related to what I need? And if so; is there a way to commit folders from PHPStorm without it "thinking" I want to commit the whole project?

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