If git complains with this error:
fatal: bad object refs/remotes/origin/HEAD
error: failed to run repack
This may happen if upstream branches have been removed and your origin is pointing to it. You can confirm this by running:
cat .git/refs/remotes/origin/HEAD
If it is pointing to a branch that doesn't exist,
Running git remote set-head origin --auto
followed by git gc
will fix it