Intermediate commit: flag command, new taxonomy formats working, etc
Catch-up merge of origin/master
Integration of taxonomy from study 713
Tweak the README
Catch-up commit bringing in changes from branch master
Fix synonym processing; implement prune command; fix problems in the patch files
Added Silva; directory layout improvements; pay attention to column names in synonyms.tsv; redo and fix rank conflict detection; sanity checks on ranks
Permit taxonomies to be forests
Intermediate commit, continuing work on Silva
Full accession id to NCBI taxon id map for Silva.
Revamped command loop to make --select preserve ids when there's only one input taxonomy.
Taxon ids are now arbitrary strings, not just integers (for Silva).
Source ids are now carried over from source taxonomies and edits into the OTT taxonomy file.
Add 'hybrid' as trigger for 'hybrid' flag.
Overhaul synonym processing to get more matches.
Add column to deprecated.tsv giving replacement ott ids for merged synonyms.
Revamp node matching rules again, for Silva.
Numerous internal changes.
Final commit (I hope) for OTT version 2.3.
Includes Silva and the study 713 taxonomy.
Added 'about' files (metadata), one per taxonomy.
Various warning message cleanups to help with debugging IF.
Added various contaminated samples to Silva taxon kill list.
Merge pull request #140 from OpenTreeOfLife/ott23

OTT 2.3