https://drive.google.com/file/d/0B0yPt9F6jiAbc3Q3M2tEclZ4MWs/edit?usp=sharing

I changed the way that rules are parsed and applied, and got all of the unit tests working. Right now, you should be able to do metathesis like

CN > $2$1

in order to reverse the order of two segments. You can also do longer-distance things like

CVN > $3V$1

which will swap C and N but leave V; the statement CVN > $3$2$1 is equivalent in this case. Just remember that the index number after the $ sign counts every variable, and starts at 1.

It should be fairly easy to add further functionality so that

CN > $2$G1

will be possible, so that you can (in this case) do metathesis and change voice at the same time, provided of course that G and C have the same number of elements.