Adding --copy-numbers to `guppy mft`.
Lengthening branches on the first pass through the tree.
Keeping track of what's being renumbered.
Adding Newick_gtree.consolidate.
Refactoring to Placerun.unitize; adding Pquery.translate_pql.
Adding `guppy trim`.
Moving ll_normalized_prob; adding Pquery.renormalize_log_like.
Keeping track of discarded reads in `guppy trim`.
Forgot to add a specl for --discarded.
Fixed the branch lengths in transm from Newick_gtree.consolidate.
Adding a `transm` attribute to placeruns.
Fix various guppy commands to operate on trimmed trees with a refpkg.
Appropriately scaling mass across names in Pquery.set_mass.
Fixing add_zero_root_bl; calling it before consolidate.
Changing the implementation of Voronoi.combine_solutions.
fixing min_min bug in Voronoi.combine_solutions
Fixing the criterion for adding new solutions.
Merge branch 'dev' into 231-cdd
Merge branch 'dev' into 216-guppy-trim

Conflicts:
	pplacer_src/guppy_commands.ml
	pplacer_src/guppy_pca.ml
	pplacer_src/newick_gtree.ml
	pplacer_src/pquery.ml
Docs for guppy trim