Pre commit hooks running but PHPSTORM dont commit changed files by csfixer

Hi there, 

Like in topic I have problem with git and storm, I dont know why but my pre commit hooks running well when I'm using console git, before commit I have running tests and php cs fixer clean up mess in files, then every change by csfixer is comitted. When I'm trying to make the same with storm overlayer on git with ticked "git hooks" option I tests runing, cleaned in files but changes that cs fixer made is not commited. Maybe u know what I'm doing wrong?