Do not add transitive dependency to deployments for system dependencies or user dependencies

Currently the ModuleSpecProcessor adds transitive dependencies to a deployment if the module spec is specified to add them (looks like only RAR's from what I can see). This includes transitive dependencies that are declared in a jboss-deployment-structure.xml or ones automatically added by the container.

Change to only allow class-path entries to be transitive if the module spec defines they should be. System and user specified dependencies should not be transitive.