test files
Merge branch 'master' into structalign
model extension framework, part 1
axes & rots fix
For Adam to check apache import.
Include commons-math3 missed in previous commit.
replaced commons-math jar with snapshot version
missing jar added
First version of columnContrib for likelihood of structural alignment.
handling tree topology change in StructAlign
edge length change
added Vertex.index
Added function to calculate covariance between all leaves of tree.
Merge branch 'structalign' of https://github.com/statalign/statalign.git into structalign
Update covariance function to use Vertex.index.
model extension framework, part 2
RNA mode discovery restored in GUI mode
Merge branch 'master' into structalign

Conflicts:
	src/statalign/base/Mcmc.java
file reader fixes and model extension for GUI
Merge branch 'master' into structalign