Remove the mrcaMatrix invariant from GNJ.
line was not set to NULL
Another 5-10% off the running time

From using the new recon functions and making getLeafToSpecies a
little more sane.
Use new "matrix diff" stuff, although it doesn't make a huge difference
Speed up matrix index->join cost index hash creation
remove profiler stuff so it actually compiles
Fix memory leak
Merge branch 'phylogenyGreedySplitAndRescue' into outgroupDepth

Conflicts:
	bar/impl/rescue.c