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If you're using Workbench 3.1.1, the app has to have the AppConfig definition that works with 3.1.1 Tools and Frameworks. Use the Deployment Template bundled with 3.1.1 to create an app and copy the Discover-PCI pipeline into that app (and any other assets needed).
See my thread from earlier in the week: Tools & Frameworks with ExpMgr 3.1.1 doesnt have instantiated applications
I believe I was using T&F 3.1.1 RC3 to deploy. After re-downloading the latest T&F 3.1.1 from edelivery, it now works. Thanks for the help.