Merge branch 'master' of github.com:OpenTreeOfLife/treemachine
fixing dead ends
minor changes
actual delete
added name output in test
ignoring .orig files
merging
Merge branch 'deadends' of github.com:OpenTreeOfLife/treemachine into deadends
just a comment
changes for jsons for nonargus things
plugin for d3 viewing
more json updates
more jsons
added for json focal node
merging
gitignore
Merge branch 'deadends'

Conflicts:
	src/main/java/opentree/GraphExplorer.java
	src/main/java/opentree/synthesis/RankResolutionMethodInferredPath.java
	src/main/java/opentree/synthesis/ResolutionMethod.java
more merging
corrected after merge
Merge branch 'master' of github.com:OpenTreeOfLife/treemachine into synthesis_organization