One indeed has to choose Add a Resource > URL in order to replicate 1.9 behavior and link to the files in the Repositories.
Plus, if you Allow External Links for the installation, then you can use Insert/Edit link or image icons in the text editor - and can also link directly to some repositories.
However, repositories behave differently: some of them are set to allow linking, others are not; plus not all of them appear all the time in the File Picker. It depends on your starting point.
I do not have all repositories in place, so here is my list based on our local install and on qa.moodle.net. Moodle 2.0.1+
Please add your experience
Add a Resource > File (copying from repositories)
- Server files ( I guess it is not really a "repository", but it still stores files) – Shown. Copy.
- Legacy Course Files – Shown. Copy.
- Private Files - Shown. Copy.
- WikiMedia - Shown. Copy.
- YouTube - Not Shown in the File Picker
- GoogleDocs - Shown. Copy.
- Picasa web album - Shown. Copy.
- Flickr - Shown. Copy.
- URL downloader - Shown. Copy.
- WebDav - Shown. I see my folders from there, but I do not see any files inside (we are still working on this), thus not sure in the behavior
- Merlot.org - Not Shown in the File Picker
- Dropbox – Shown. I do not see any files there, not sure in the behavior
- Alfresco - ? ?
- Equella - ??
Add a Resource > URL (linking to repositories)
- Server files - Not Shown
- Legacy Course Files - Shown. Link.
- Private Files - Not Shown
- WikiMedia - Shown. Link.
- YouTube – Shown. Link.
- GoogleDocs - Not Shown
- Picasa web album - Shown. Link.
- Flickr - Shown. Link.
- URL downloader - Shown. Link.
- WebDav - Shown. I do not see any files there, not sure in the behavior
- Merlot.org - Shown. Link.
- Dropbox – Not Shown
- Alfresco - ? ?
- Equella - ??
Insert/Edit LINK in the text editor (both copying and linking)
- Server Files - Shown. Copy only
- Legacy Course Files - Shown. Both link and copy
- Private Files - Shown. Copy only
- WikiMedia - Shown. Both link and copy
- YouTube - Shown. Copy only
- GoogleDocs - Shown. Copy only
- Picasa web album - Shown. Both link and copy
- Flickr - Shown. Both link and copy
- URL downloader - Shown. Both link and copy
- WebDav – Shown. I do not see any files there, not sure in the behavior
- Merlot.org – Shown. Copy only
- Dropbox - Shown. I do not see any files there, not sure in the behavior
- Alfresco - ? ?
- Equella - ??
Insert/Edit IMAGE in the text editor (both copying and linking)
- Server Files - Shown. Copy only
- Legacy Course Files - Shown. Both link and copy.
- Private Files - Shown. Copy only
- WikiMedia - Shown, both link and copy
- YouTube – Not Shown
- GoogleDocs - Not Shown
- Picasa web album - Shown. Both link and copy
- Flickr - Shown. Both link and copy
- URL downloader - Shown. Both link and copy
- WebDav – Shown. I do not see any files there, not sure in the behavior
- Merlot.org - Not Shown
- Dropbox - Shown. I do not see any files there, not sure in the behavior
- Alfresco - ? ?
Moodle Media in the text editor (both copying and linking)
- Server Files - Shown. Copy only
- Legacy Course Files - Shown. Both link and copy.
- Private Files - Shown. Copy only
- WikiMedia - Shown, both link and copy
- YouTube – Shown. Copy only
- GoogleDocs - Not Shown
- Picasa web album - Not Shown
- Flickr - Not Shown
- URL downloader - Shown. Both link and copy
- WebDav – Shown. I do not see any files there, not sure in the behavior
- Merlot.org - Not Shown
- Dropbox - Shown. I do not see any files there, not sure in the behavior
- Alfresco - ? ?
- Equella - ??
P.s. Back to the original question from Sam - I am not sure why Alfresco is not shown in the File Picker for the URL resource :/