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It would be really helpful to go into some detail on the steps taken to clean up the git history.

It isn't what they did, but my recommendation for most such use cases is the BFG Repo-Cleaner: https://rtyley.github.io/bfg-repo-cleaner/

Don't be deceived by the "java" invocations, it's written in Scala, so it's HN-approved!

Removing directories is simple.

But you can do almost anything via custom scripts.