I was experiencing a bit of a problem with some conflicting files on google drive and a github repository. I mirror my google drive as my Documents folder and on occassion, I am logged into more than one machine at a time and if you work on the same files without saving, they result in a conflict. I notice this when I got the message.
Office-iMac:gstudio rodney$ git pull fatal: Reference has invalid format: 'refs/heads/master[Conflict 1]'
And then when I looked into my .git folder, I saw
Office-iMac:gstudio rodney$ cd .git Office-iMac:.git rodney$ ls COMMIT_EDITMSG index COMMIT_EDITMSG[Conflict 1] index[Conflict 1] COMMIT_EDITMSG[Conflict] index[Conflict 2] FETCH_HEAD index[Conflict 3] FETCH_HEAD[Conflict 1] index[Conflict 4] FETCH_HEAD[Conflict] index[Conflict 5] HEAD index[Conflict] ORIG_HEAD info ORIG_HEAD[Conflict] logs branches objects config packed-refs description refs hooks
Apparently, git does not like square brackets and such in the names. To fix this, you need to do the following.
find .git -type f -name "*Conflict*" -exec rm -f {} \;
And then clean up the packed references as:
awk '!/conflicted/' .git/packed-refs > temp && mv temp .git/packed-refs