Metathesis might not actually be too difficult, though every time I've thought some thing like that I've been wrong. I get the feeling that the solution lies somewhere inside a LinkedHashMap, which might be a good way of doing this one thing in general.

Right now I'm finishing up adding support of legacy segmentation (that is, no special segmentation) and normalization control. The test version used canonical decomposition, and future versions will do so by default, but you can turn it off, or use NFC, NFKC, NFDC if you need to.

After that, I need to add support for negatives in the rule condition (just on variables and literals for now). I have an idea of how I can do this on sets and subexpressions, but since I literally got stuck on this for SIX MONTHS I'm managing my expectations.

But seriously, don't we all want to live in a world where

a e o á é ó > ā ē ō â ê ô / _{s n?t r l m}-s#

or

CH > J / _R?VV?C*CH

is a valid sound change expression?

Also, I probably should get this onto Github or something.