Removed unused code, updated deps.

Summary: This removes some stuff I ported from mr that is either too messy for prime time or supplanted by stuff we've done since. Also, I updated the README's installation instructions.

LinkOnDisk and Trajectories were supplanted by framewise_data.py

This removed the dependency on yaml_serialize, which was no longer
actually used.

I will restore the wire-tracking code when it is in better shape.