JavaRunner: make sure everything from system repo + flat repos is considered in the classpath #488: Ceylon embedded runner

Otherwise we would add system repo jars in the url class loader because they come from non-flat
repos
Test that we only have a single jar in the url CL for #488: Ceylon embedded runner
Tool API: added RuntimeOptions #488: Ceylon embedded runner
Tool API Runners: support extra modules #488: Ceylon embedded runner
Tool API: test loading of extra modules #488: Ceylon embedded runner