submodule problem fatal: Not a git repository:

Hi All.

I have latest version of PhpStorm.
I've created new project from my existing files.
Now I want to change branch but this is not possible because of submodule problem.

Couldn't checkout develop
fatal: Not a git repository: /vagrant/www/abc/.git/modules/typo3conf/ext/my_new_extension  

I have no problem with changing branch under shell or aptana.

Any idea what is wrong?