Bugs are positioned to one side of the path. They should probably be positioned relative to the center of the path (i.e. evenly distributed on both sides of the line), or even directly on the line as they were before.
Levels seem to be much quicker on this branch. Not sure if this was intentional, or even where you changed this (I looked over the diff a couple times, and couldn't see any change that looked relevant).
I managed to get a crash where I got an allele with a target field that had a value of undefined. It crashed on line 175 of allelePointSystem, but it looked like the real problem was somewhere else, like in the allele generation code. Not sure if this is unique to your branch, so I wouldn't worry about it too much if you can't repro or can't think of something that might of changed (I couldn't see anything that looked relevant in the diff).
Most minor changes with a far reaching affect.
Fixes #123, #122, #121, #116, #107