When you run the git pull command on linux, you may come across a bugs that if one file or directory has permission problem. Once the permission (or any access I/O) problem comes out, the files' modification date before the error may changed to current!?
Then, what happen? Once you fixed the access or I/O problem and run git pull again, thousands of conflict come out because of the file date changed.
This problem is impossible to recover. Good practise is BACKUP, always. Make a good ignore list. Remind yourself to fallback the write permission of the files and directories before.