First commit of java code part.
Modified the spec to introduce a SpeciesTree type and supporting types.
Merge remote-tracking branch 'origin/species-tree-spec' into dev
Added a couple functions to the tree spec to support building a SpeciesTree.
Next modification. Still not ready.
Merge branch 'dev' into species-tree-spec

Conflicts:
	Tree.spec
Modified Tree spec file.
Merge remote-tracking branch 'origin/species-tree-spec' into dev

Conflicts:
	Tree.spec
Merge branch 'dev' of git.kbase.us:trees into dev

Conflicts:
	Tree.spec
Next modification of service.
Tree service java part is ready to be deployed together with perl part.
some makefile edits for the perl service start/stop scripts
removed new methods from Tree.spec because they are not in the perl server
Refactoring related to change of module name in java part.
Checking code for calling dev-instance of tree service.
Parameter for fast tree construction (based on ribosomal S9 protein
family only) mode was added which is useful for testing.
updates to deployment steps, still needs some work though
basic deployment seems to work, needs more tests
working deployment, test updates are needed next
Added code to generate mapping between NCBI taxonomy ids and KBase ids.