I don't have this in my brain anymore so definitely take my thoughts here with a grain of salt.
I think the general approach would be for external apps to hand Collect URI(s) to form definition and/or media files with permissions through an intent extra. I vaguely remember giving some thought to where this should go and I think my conclusion was that it should be a new, dedicated activity that takes whatever URI(s), copies the files into the Collect directory, registers them in the database and generally gets them ready for use.
Even though you're only looking to register media files (in this case a CSV) with Collect, I think the solution design should also include registering a form definition. Those are tightly related and we'd want to make sure that they're handled coherently. Additionally, whatever we come up with, we should then later be able to add something symmetrical for handing submissions to Collect.
Would be great to see some of your ideas.