I am doing a complex PHP project with two other people. We had git setup for the project from the beginning.  After working for two months, we wanted to remove certain folders (/dev/app) from git tracking ( git was already tracking them). So I deleted all the files from /dev/app and added a entry in the .gitignore file to exclude the PHP files in the /dev/app folder. 
**/dev/app/*.php
I made a commit to the master branch. I pushed them to the origin and it was working fine. But my colleagues were working on different branches. When I merged their branches with the master, git started to track the excluded files again.
In the local environment it is not a problem, but in the production environment it is a huge headache. I only need the client generated files in the /dev/app folder in the production server, and I need to preserve them without any modification.
can anyone help me to overcome the issue?