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What to do when .gitignore doesn't

So. At work we’ve switched from using svn to git (and GitHub). Difference: decentralised, therefore “commit” commits it to the local repo rather than the remote/centralised one, and you have to “commit” then “push” to the remote. Problem: .gitignore was not gitignoring some files (settings.php and .htaccess which I had to change to make it work on my local) which it was supposed to be gitignoring. Solution as per