Running a git status command shows modified files, with only changed file permissions. This can be due the IDE, for example PHPStorm is known for being a bit too nosy.
diff –git a/myproject/index.php b/myproject/index.php
old mode 100644
new mode 100755
Git configuration contains an entry that defines if file permission changes should be considered as changes or not. Do disable this, just run the following:
git config core.filemode false