If you’re doing something that needs to change its directory to another place (like say, you have the unfortunate need to call an external repository to perform a subtree merge after your repository has been updated), the variable GIT_DIR needs to be unset for things to work properly.
Do:
unset GIT_DIR
in your bash script to make this happen.
References:
http://www.kernel.org/pub/software/scm/git/docs/howto/rebuild-from-update-hook.txt
It needs more code 