Start to separate up/down phases for segment mapping
framework mostly there, but still a ways from working
Most existing unit tests passing.
Existing unit tests all pass.
Extra unit test for checking the new functionality.
get rid of debug prints
Self-snakes should work, probably.
Fix other programs that used the old spanning-tree semantics

also change the names to clarify.
Cleanup changes
Merge branch 'mapWithExtraParalogs' into development

Conflicts:
	api/tests/allTests.cpp