Serializing nodes base on ids instead of names. Creates connectionNode
and connection in schema.
add connections to entity in schema
Serializing connectio node and adds test
more work on connections
fix serialization assert
Merge pull request #38 from openworm/connections

Connections
fix recording reference
Merge pull request #39 from openworm/connections

fix recording reference
Minor changes for easing model tree population
Merge remote-tracking branch 'origin/development' into neuromlpopulation

Conflicts:
	src/main/java/org/geppetto/core/model/state/visitors/SerializeTreeVisitor.java