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Ok, I closed Architect, and manually added my new controller to the Application file in metadata. Opened up Architect and now that controller was added as expected.
I'm not sure how that metadata stuff is handled, maybe it was just chance that things worked after a restart (but they hadn't previous to this).
Also, my controller stopped saving, so I closed Architect, manually edited the controller in the metadata folder, reopened, and now it's saving my changes again.
Any more hints to reproduce this? Have you seen it any additional times?