How to ignore not changed files to "git commit" in PhpStorm

I have a new branch from dev, make some changes and want to commit and push, when i press commit there are all files of project, changed and identical, all... How can I exclude not changed files? (PhpStorm 2018.1, Ubuntu 16.04)

git status

shows that all files are modified too

Also, i noticed, that the files were with a modified permission, so I exclude they with command git config core.filemode false