How to restore version control in XCode?

Question

I have just recently backed-up my XCode C++ project on my pendrive, using

rsync -avu 

Since then, the version control for my project is lost (grayed-out) on every files, I can modify the files and not see the "M" nor the "A" sign. The only files still having version-control working "shared" files for which it works correctly. (Those shared files belong to a different project called "Shared").

I have tried git commit -m, git add . and even git init where the files were. Nothing worked.

Can you please help restoring version control for my project?

(Is this rather an SO question?)