Before proceeding, make sure all your changes are committed, including your .gitignore file.
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.
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.
git add .
git commit -m ".gitignore fix"