This is discussed more in PR #140773.
The cause of the breakage was the change of the Manifold library
version from 3.0.1 to 3.1.0. That change is very positive otherwise
because we can remove the "use runids" workaround to prevent bad
face merging, and that removal is also part of this commit.
Removing that changes the time to do a big sphere-sphere test
from 660ms to 340ms.
The problem that needed fixing is that the new library version appears
not to do some aggressive simplification that the old version did,
and as a result, when we dissolve triangulation edges after the boolean
is done, it sometimes leaves valence-2 vertices on original edges.
To fix that, new code detects and then dissolves such vertices.
ea65aa5ea1