In the remote server I have a post-receive hook set up in order to make a git checkout of my repository:
#!/bin/sh
GIT_WORK_TREE=/var/www/ git
Also remember to check permission of root directory itself!
You may find:
drwxr-xr-x 9 not-you www-data 4096 Aug 8 16:36 ./
-rw-r--r-- 1 you www-data 3012 Aug 8 16:36 README.txt
-rw-r--r-- 1 you www-data 3012 Aug 8 16:36 UPDATE.txt
and 'permission denied' error will pop up.
After checking the permission of the folder, it is okay with 744. I had the problem with a plugin that is installed on my WordPress site. The plugin has hooked that are in the corn job I suspected.
With a simple sudo it can fix the issue
sudo git pull origin master
You have it working.