Disallow newick trees with implied roots

(i.e. branch lengths on the root node)
Causes confusion since it creates an extra node, even though it's
allowed in the newick standard
Fixes benedictpaten/cactus#5
Merge branch 'development' of https://github.com/benedictpaten/sonLib into development
Make adding implied root nodes optional to fix tests
Merge branch 'development' into phylogeny