Your memory is of something THAT DID NOT HAPPEN... the journal articles are available on the internet, if you know how to search for them... and the all refer to Apple working WITH Digital Research to handle the infringement issues. Atari was never SHUT DOWN... in fact Tramiel of Commodore fame bought Atari for a song because it was losing money from a conglomerate and he thought that Atari had the Amiga... but they had defaulted on the second payment for the Amiga and his prior company Commodore had snatched up Hi Toro. So he quickly raided Commodore for some engineering talent, filed the serial numbers off CPM, renamed it Tramiel OS, bought some GEM licenses for a shell, and released the Atari 520 ST with little problem, BEATING the Commodore Amiga to retail market by a week. Apple did not have a problem with either companies' offering... They objectected Digital Research's GEM copying of MacOS copyrights and patents. This was done by November of 1985... and everyone was happy.
Again this is from memory from journal articles at the time, my memory is still good enough to earn a living with, maybe the journals were all lying, but you don't have to look terribly far for evidence of Apple being a company which tries to earn its living in courtrooms, there's an account of something like that in the news on FR today
Again from memory, the Apple/Atari thing included a claim of primacy on the idea of using a trash-can icon for deleting files which is like Ford claiming a patent on the use of steering wheels to control cars. In fact given the origin of the GUI at Zerox-PARC, what you're really talking about is chutzvah.
Again this thread is not about ancient history, it's about Apple marketing products which can't make it halfway to the 2-year trade-up point or, at the very least, one of which didn't.