Overlap removal improvements.

Attempt a fix for the overlap removal problems by adding functionality for consolidating duplicate and near-duplicate intersections.

This addresses #473, #488, #496, and #729.

Output is extremely verbose right now. I plan to disable most of that before merging.

Due to the large structural changes in the overlap removal functionality, I would strongly encourage anybody who uses it to test the branch overlap_exploration_2 extensively and to report back to me in the next week on any problems.