I've been using 'Mu4e' for the past few years and recommend it: http://www.djcbsoftware.nl/code/mu/mu4e.html
https://github.com/agpchil/mu4e-maildirs-extension
It didn't work quite like I wished right "out of the box", but it wasn't too hard to hack it to behave more according to my wishes. Three cheers for open source software!