This is probably my fault...however, I don't know what to do now.
I have two sites. One is moodle 2.1 from new. It has a repository directory in the moodle data folder I set up in the root of my server. No problems, works well enough.
The other site was 1.9 untit today. In order to covert some courses from 1.9 to 2.1 which simply refused to move between the sites any other way, I upgraded the site to 2.1. I then planned to backup all the courses in the mbz format and move them to the desired site.
I went looking for repository in the original moodle data folder for the 1.9 site and realised it wasn't there. So, I created one and added a few folders. Then I added the repository instances. Then I went to see what was where.
I backed up a course, then couldn't find it. Curious, I searched the site and found that I have a repository folder (with all the relevant folders like alfresco etc) inside my main moodle folder. It's moodle/repository/ to be precise. Is this normal? I thought repository was set up by moodle in the assigned moodle data folder? It's not the end of the world, but I would imagine that 2 repositories will tick moodle off at some point. How do I fix it? As I upgraded, I believe the data for my old courses must be in legacy folders.