I have the following .gitignore file
# file named .gitignore
shin@shin-Latitude-E5420:/var/www/myapp$ git status
# On branch master
# Your branch is ahead of 'origin/master' by 1 commit.
# Changes not staged for commit:
# (use "git add <file>..." to update what will be committed)
# (use "git checkout -- <file>..." to discard changes in working directory)
# modified: modules/recaptcha/config/recaptcha.php
# modified: system/application/config/config.php
no changes added to commit (use "git add" and/or "git commit -a")
The files are already stored in your local commit tree. You need to remove them from the repository this can be done via
git rm --cached system/application/config/config.php modules/recaptcha/config/recaptcha.php after that you need to make one more commit and your good to go.