Completely remove files from Git repo and remote on GitHub

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This is what you’re looking for: ignoring doesn’t remove a file. I suggest you read that page, but here’s the specific command to use:

git filter-branch --index-filter \
'git rm -r --cached --ignore-unmatch <file/dir>' HEAD

Also, to remove all the deleted files from caches git creates, use:

rm -rf .git/refs/original/ && \
git reflog expire --all && \
git gc --aggressive --prune

You can find more info about the last command, as well as a script that does everything you want in one single action, here: git: forever remove files or folders from history.

Another links with lots of explanation: Remove sensitive data.

[Edit] Also, see this StackOverflow question: Remove sensitive files and their commits from Git history.

(Commands copied from natacado‘s answer in the question linked above.) If you have already removed the files from the working copy, the following should work. Find out the hash for the commit that added the unwanted files. Then do:

git filter-branch --index-filter \
'git update-index --remove filename' <introduction-revision-sha1>..HEAD
git push --force --verbose --dry-run
git push --force

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