If we want to completely remove a file from github - including all history - there is a tool that we can use called the BFG.
The github help article is here:
And the BGF itself is available here:
We'll start by downloading the BFG jar file, and then cloning a mirror of our repo with:
git clone --mirror [repo-url]
Then we can delete our .env file with:
java -jar ~/Downloads/bfg-1.13.0.jar --delete-files .env my-repo.git
which will delete the .env file. Then we can use the following command to prune the entire history and garbage collect the remains:
git reflog expire --expire=now --all && git gc --prune=now --aggressive
And finally, use
git push to push that change to github, and remove the .env file from all of the history on github as well.