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Most people just use Sonarr/Radarr for this, though it can be tricky with anime specifically because you are pretty much locked into TMDB metadata, which might not be what you want for some series (alternate orders, absolute or series numbering, season 2/3 being different shows entirely, side series being specials not a season etc. etc. etc).
I've used TinyMediaManager before, not open source (other than a very old version that is still out there last time I checked), but the free version is reasonably powerful, especially if you want to customise the details of your naming/folder structures or do custom metadata or ordering. has some CLI functions but is mostly intended as a gui app.