PhpStorm + git 'Contents are identical' why?

Question

PHP

In general, the problem is this. I will describe a typical situation that repeats itself over and over again.
There is cms, which is developed by itself, of course, all with the help of git (github). There is a site that is based on this cms (all changes are tracked again using git). But here they released a new version of cms, they decided to transfer the site to this newest version.
In general, some files were updated in cms, and most remained untouched. We download the archiver with files from cms, delete the folder with cms from the site in order to cleanly unpack the files from cms.
So now we open the site in phpStorm, it updates the data on the files and shows us that absolutely all files have been changed, even those that were not touched. I try to look at diff files, but they are the same, up to the end of the lines, and phpStorm writes 'contents are identical' to such files when diffing.
Those. phpStorm writes that the files are the same, but still marks them as modified. Or does it tag git? And how to get rid of this problem?

Answer 1

I'm on Linux. The problem was that git was trying to preserve file permissions. I solved the problem by changing in the .git/config file :
For anyone else, I put:
git config --global core.filemode false