Fix inconsistent merging of asymmetric hole overlaps.

When computing the overlap relation between holes with different
sizes, the current search may not find all overlaps in the case
where a smaller hole is visited before a larger one, because
searching for holes within the radius of the smaller hole could
potentially not find the larger one.

The search procedure is altered slightly in order to solve this.
First, we begin the search by looking at holes in descending tool
diameter, to give a known upper bound at each stage.

Then we find potential overlaps by finding all holes within this
upper bound, and select the results that actually overlap.