Planning for specifying color per-shape.
Reorganize pen.py and add color property.

- Reorganize pen.py into sections.

- Add pen.set_color, and carry color information into the generated
  segments and shapes.
Added color specification to shapes.
Added rectangle shape.
Refactor paths to be just another type of shape.

- Add support for overlapping shapes and paths.

- Add support for differently colored paths.

- Move path related code into a new file, path.py.

- show_bones, show_nodes, and show_joints now are set on the Pen class,
  not on Paper.

- Paper.center_on_x is currently broken.