OK, that is interesting, but doesn't do what I want at all.
I want to, for example tell sonarr that the file "flugbottle.mkv" in "Series Name/Movie" should be treated as "Series Name S00E14 - The Battle for Flug Bottles" WITHOUT having to rename the file or having to move it into "Series Name/Specials".
It looks like the only way to do that is to hard link the file from where I want it to where Sonarr insists it has to be, which also means not being able to do it through the webUI, but having to ssh in.
There's no reason that sonarr has to enforce a directory structure. It shouldn't care at all where the pointers in the database lead.