here are the answers to your questions:
1) all of it is left; but we did this on purpose for this first iteration (you may notice you can only deactivate a module, but can't delete it). Namely, removing the module is not a trivial task, as many scenarios come up and we need to provide users with options to fine tune this process. For example, do we delete database objects or not? Do we delete the data? What if you've spent 3 weeks entering data and someone deletes it? If you delete the module, you may presumably want to export the data before you delete the module. Those are only few to note.
Now, all this being said, it is among our top priorities to implement this as, it may be annoying to say the least, but we have opted for the less dangerous approach (annoyance always beats the irreversible damage to site). It's hard to say at this moment, when exactly will this be released, but I'd say that next major release in February should be it (we may try to push it earlier through internal builds). Also, worth nothing, once available, this feature will be able to completely remove the modules you create with the current version.
2) Yes, this is our next major milestone. We are aiming at a very decoupled architecture here, so something along your guess is probably what we will end up with. What I can say with certainty is that it is going to be future-proof. In all honesty, this is already possible - the code actually supports it (e.g. media fields are actually doing this very same thing, but linking to the 3 specified types of the libraries module: document, image and video) - but we need to put a lot of thought into how will this work in the user interface. While selectors could work, our plans are actually a bit more ambitious - we want to create a native flow in the backend user interface as other modules have (think blogs for example).
Hope this answers your questions.
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