Github setup via git on development server

Previously, I had set up phpstorm to a copy of a repo hosted on a linux server.  We would have our golden repos in one area on the server, then we would clone to our own development area, then open a new project to our development area in phpstorm.  We would have to set automatic deployments to save changes to our dev environments on the server to reflect changes.

Currently, I'm trying to configure phpstorm to access the same setup, except instead of the golden repo being on the server, it's a github remote repo that's cloned into my development area.  I was able to start my new project using my development repo and everything looks like it's working fine, but it's not.

I knew there were changes in dev from other devs, so I did a git pull.  phpstorm reported zero changes.  Long story short, I was able to git pull at the command line of the development server, and THEN git pull in phpstorm to get all the changes.  Does this mean that I will need to do all the git commands in both the command line AND phpstorm?