We wil be moving to 2.2(plus) this summer from 1.9.12. I am planning out our internal Moodle repository folder structure so that it is as well designed from the begining as possible. I think I understand it well enough to set that up in our test Moodle, but I am wondering how using internal Moodle repositories impacts a course that is shared later with other Moodle organizations. Will a course package up all the varied files needed from the repository folders and carry them internally to the new Moodle or would the organization need access to our internal repository to use the course in their institution? Information about this may impact whether we use an internal repository or set up an external one. We definitley want to be able to share what we build as well as have the courses stand on their own in case our project fades away in some future year. We would hate for another institution to have to rely on our survival to use a course we pass on to them. I appreciate all of you who are several steps along the path further than I illuminating the path for those who follow behind. :0)
You may want to have a read of this white paper that I wrote about repositories in Moodle2 - http://www.somerandomthoughts.com/blog/whitepaper-moodle-2-repositories/
The core of your question is one of the core issue with repositories.
When you do a backup-restore to share with other institutions or even the public you need the resources which are in the course to be shipped with the course (in the zip) or at least there should exist public access to them. When you embed a Youtube video for example it is just the embed code you ship, as the youtube video is public.
As it stands (you will see in the whitepaper feature breakdown) when using the repositories that come with Moodle 2, Moodle will copy the file into the Moodledata space and Moodle only offers the option to link to the file in the repository where the API allows it (which assumes direct public access to the file).
So if you hook up any repository out of the box with Moodle, when you add it to a Moodle course it will copy the file into Moodle to ensure integrity of the course.
There are some non-core repository options which store the files in the repository and not in the moodledata - Equella or ELIS for example which are premium offerings. These are good tools that provide great workflow and tight content controls for where you dont want to have a backup being the full snapshot of everything in the course.
Hope that is of some help!
Another possibility could be to provide a copy of the repository along with the course. It could easily be added to an organization's repository system. It would need to be relative linked instead of keying in on the full url. Does anyone know if the repostory system set up insite the data foder is relative?
For some of what you desire to do (sharing), might check into a Moodle HUB:
'spirit of sharing', Ken