Found what was wrong. I don’t understand how, but .git directory path somehow was changed to other path than I was working in. So then anything I changed was not checked, because git was checking in other place. I noticed it, when I reinitialized it and it showed that it reinitialized entirely different directory. When I cd .. from my current directory and cd to it back again and then reinitialized yet again, then it switched back to correct .git directory and started seeing my changes.