Refactor to clearly delineate generated and custom code in case we need to re-generate due to database changes

Conflicts:
	seqware-admin-webservice/src/main/java/io/seqware/webservice/controller/CustomWorkflowRunFacadeREST.java
	seqware-admin-webservice/src/main/java/io/seqware/webservice/controller/ModelAccessionIDTuple.java
	seqware-admin-webservice/src/main/java/io/seqware/webservice/generated/client/SeqWareWebserviceClient.java
	seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/plugins/deletion/DeletionDB.java