Fixes #1643: The GML Reader can now parse arrows from the old galFiltered.gml and yEd files properly.

Change-Id: I33575d8793c9fb491dd6930901ff7a084f2bd801
Updated file naming scheme for downloaded apps, no longer checks for updates of uninstalled apps, downloaded app names now contain version.

Conflicts:
	app-impl/src/main/java/org/cytoscape/app/internal/ui/InstallAppsPanel.java

Change-Id: I8b7dee371207a522925640045deb0243dba35994