Various fixes part deux.

• Get some of the CMB tests working by writing the .plugins file to the proper location and updating some baselines to deal with transparent selected-entity rendering.
  • The test of multiple models with different representation coloring modes can't work until the discrete session's read operator is fixed (it currently provides no tessellations).
  • The test of the model tree won't work until the polygon session's read operator is fixed (it currently reports all cells as free cells rather than just the faces).
• Improve packaging of the new modelbuilder app. This does not get everything working, but fixes a lot.
• Add in some skeleton documentation so read-the-docs can choose happiness.