Step 1. Switch to your branch
Strp 2. Remove files using -rm command
Ex : git rm -r sites/all/modules/stage_file_proxy
Step 3. Add this file to the .gitignore
Step 1. Install Xdebug
If not already ainstalled, Install Xdebug (I'ts already on the package WAML, LAMP, MAMP)
In Linux Debian/Ubuntu/Mint # sudo apt-get install php5-xdebug