Running mac off internal HD, how can I revert back?(mac noob)

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I recently had a bit of a disaster trying to install catilina on an unsupported imac 13,1 late 2012. I ignored the idea of backing up for some reason and wiped the entire computer(wasn’t really bothered) the problem before it said my internal hard drive has s.m.a.r.t errors, so I presumed the internal hd was broke. My mac was stuck on recovery mode and I was panicking after messing about I managed to install catilina! I was on elcaptain before, turns out I installed this onto my external hard drive n didn’t utilise any off the internal HD. There seems to be no problems with the Internal HD now, so basically my start up disk is my external I think and it has all the important files on my external, I tried to transfer the files back over to my mac on my desktop(mac noob) and “the folder ‘system’ can’t be moved into one of its subfolders” I ran first aid to make sure my internal HD was bugging out and not saying it’s broke but the first aid didn’t pick up on anything. Is there anyway I can revert to using the internal HD to run everything?
 

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