Refactoring: moved some of plug-in level methods and objects into a new
class, org.reactome.cytoscape.util.PlugInObjectManager.
Finished loading pathway hierarchy, pathway overview and loading pathway
diagrams
Selection synchronization: partially done
Finished selection synchronization among multiple GUI components
Merge branch 'develop' into path-x

Conflicts:
	pom.xml
	src/main/java/org/reactome/cytoscape/util/PlugInUtilities.java
	src/main/java/org/reactome/cytoscape3/Config.prop
	src/main/java/org/reactome/cytoscape3/PlugInScopeObjectManager.java
	src/main/java/org/reactome/cytoscape3/ReactomeFIBundleActivator.java
Added back some code from the development branch to make 3.0.1beta
features work