Basically all this will be resolved by the Repository API in Moodle 2.0. I really don't want to hack this into Moodle because it leads to all kinds of other problems.
The idea for the future is that we use a separate repository for all user files (the respository can be all kinds of things from Internet hard drives to specialised document repository software) which Moodle accesses via a plugin to give a nice consistent interface.
This is the first priority after the Bugathon.
In the meantime, even now you can store files externally somewhere and reference them in resources using their URL. It's just more manual and less secure than the repository API will be.
Resource types
Linking resources between courses
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