Added removeGenome and insertGenome methods
Merge branch 'development' of git://github.com/glennhickey/hal into development
Added removeGenome and insertGenome methods
Tools for adding/removing/inserting genomes
Add tool for replacing a genome
moved copyGenome.cpp functionality to the hal API and created tests
change modification tools to use the new genome copying API
Merge branch 'development' into modificationTools
Merge remote-tracking branch 'origin/development' into modificationTools
Append subtree utility
Rename some tools for clarity/accuracy
Set an update flag in genome metadata when modifying alignments
Merge branch 'development' into modificationTools
Add option to not mark ancestors if desired
make halStats be able to report metadata
rename metadata functions of halStats to clarify that we're looking at genome metadata
Fix halReplaceGenome bug
Make halReplaceGenome clear update flag on the replaced genome
Replacing a genome should work with all genomes now
(Other than single-genome "alignments")
Merge remote-tracking branch 'refs/remotes/origin/development' into modificationTools

Conflicts:
	stats/impl/halStatsMain.cpp