Cacher is the code snippet organizer for pro developers

Step 1: Commit all your changes

Before proceeding, make sure all your changes are committed, including your .gitignore file.

Step 2: Remove everything from the repository

To clear your repo, use:

git rm -r --cached .

rm is the remove command
-r will allow recursive removal
–cached will only remove files from the index. Your files will still be there.
The . indicates that all files will be untracked. You can untrack a specific file with git rm --cached foo.txt (thanks @amadeann).
The rm command can be unforgiving. If you wish to try what it does beforehand, add the -n or --dry-run flag to test things out.

Step 3: Re add everything

git add .

Step 4: Commit

git commit -m ".gitignore fix"

Source: http://www.codeblocq.com/2016/01/Untrack-files-already-added-to-git-repository-based-on-gitignore/