PPR design synthesis

(as of 2016-03-07) This is the original implementation of design synthesis I made back in 2013. It includes base code for topological embedding (master branch, I think), code for embedding with kinematics (kinematics branch), and code for timing analysis (analysis branch). The new_kinematics branch is old. It can probably be deleted, but I have not confirmed this, so it's still hanging around.