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
Merge pull request #136 from OpenTreeOfLife/simple-curation-app

Working tree view and editor, with clickable nodes (for re-rooting and ingroup definition)
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.
Implement configuration files; do neo4j stop/start when updating plugins
Merge pull request #137 from OpenTreeOfLife/deployment-fixes

Implement configuration files; do neo4j stop/start when updating plugins
Merge pull request #138 from OpenTreeOfLife/simple-curation-app

Proper phylogram display, w/ refresh and improved menus.
markdown docs generator script for ot neo4j services
Merge branch 'master' of github.com:OpenTreeOfLife/opentree
setting up oti
Improvements to neo4j installer; fix ; new doc file sample.config
Merge pull request #139 from OpenTreeOfLife/deployment-stuff

Improvements to neo4j installer; fix $JAVA_HOME; new doc file sample.config
Improve documentation for OPENTREE_NEO4J_HOST