Code manager setup - pulling strange modules directory
I have setup PE 2016.1.2.0 with code manager. I followed the online documentation https://docs.puppet.com/pe/2016.2/cod...
Everything seems to work fine except:
In each of my environments under /etc/puppetlabs/code/environments (e.g. ..../dev, .../production, etc.) there is a modules directory with several modules like concat, firewall, mysql, etc. Those modules are not in my control repo. When I create a new file (or directory other than modules) in my environments/environmentname (e.g. .../environments/dev) directory in my git repo then do a puppet-code deploy dev -w, it pulls those files and directories down fine. But if I put something in the modules directory in my git repo, then do a puppet-code deploy dev -w, it ignores what is in the git repo in the modules directory.
Where did this modules directory come from and how do I get rid of/alter it with puppe-code?