It's not copyright infringement, so you can just tell them to fuck off and make them sue you. If they submit DMCA, you (and because it's open source, that means anyone, today) can counterclaim and it will get put back up until they actually go to court.
It's just a lot to deal with harassment from a motivated company's resources.
I'm a little dumb and late to this so please forgive me if this is not a good question, but can you not develop an app under a pseudonym or any other way to protect your identity or was this like they tracked each dev down, got their info and legally threatened them?
Edit: I'm referring to Tachiyomi I forgot to mention that
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