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The product support manager has been in direct contact with ray_In_Vancouver. Here is the information that was provided.
The schemas themselves are usually not used in iSM. The schemas are usually part of something within a pflow. As an example, if the schema is used in START/END objects of the pFlow to expose the pflow as a WS, then during iIA creation the pflow has to be added during the “Process Business Services” wizard step and the schemas will be published and deployed automatically in the iIA.
The “Resources” step just lists everything which can be included. Note that if you select a “Channel” level component it will automatically include all the needed referenced components (pflows, transforms, etc…) The “Process Business Services” is to select available pFlows to be deployed as WS along with iIA (this will automatically deploy the schemas from start/end objects) The “Included Libraries” step is for the jars/zips needed by an application which are not available under the general iSM installation lib. For example, any of the 3rd party libs or custom libs. The “ Included Resources” step is designed to include any additional artifacts, such as scripts, property files, documents, etc… these resources will be present under “resources” folder under the iIA and can be referenced by the application as files.