@jdblair @mos_8502 I was going to mention MH. Plan 9 also did the 'mail is a filesystem' thing; when they supported MIME I think they made each MIME part a separate file, as you should (I'm not sure how they handled nested MIME parts but I'm sure they had a good answer).
MH is one of those so close yet so far things, and I say that as a very long time MH user. The idea is great, but the implementation is extremely tangled and has issues.