I think there is a bug, but I may be missing a setting. Could someone confirm if this works for you or not. I am trying to setup the File System Profile Repositories and Course Repositories so the course teacher can access these repositories.
I logged in as the Administrator, then opened Site Administration > Pluggins > Repositories > File System and checked both:
Allow users to add a repository instance into the course (can be configured only by admins)
Allow users to add a repository instance into the user context (can be configured only by admins)
I also enabled the File System Repository pluggin.
I went to my site via FTP and in the Moodledata folder, I added the folder "repository" and the sub folders "site_files", "course_files", and "profile_files". Then I added some image files to each sub folder.
Then I opened a course and as the Admin I went to Settings > Repositories and clicked <Create "File System" Instance> and selected "course_files" from the drop down list and named the instance.
Next I opened My Profile > Repositories and clicked <Create "File System" Instance> and selected "profile_files" from the drop down list and named the instance.
Then I went back to the course (still as Admin), turned on the editor, and opened the editor in a Topic Section. I clicked the Insert Image icon and both the Course Repository and Profile Repository instances are visible in the File Picker.
Then I switched Roles from Admin to Teacher and opened the editor, etc and both Course Repository and Profile Repository instances are visible.
Next I logged OUT and then logged in as the Course Teacher. I opened the editor as above and now NEITHER the course Repository or the Profile Repository instances are visible to the Teacher. THE REPOSITORIES ARE NOT VISIBLE TO THE TEACHER. I can not find a way to setup up these repositories for the Teacher Role.
If you can make this work on your site, please tell me what I am missing. If it doesn't work for you, please visit my bug report, MDL-24210, in the tracker and add your comment and vote to have this fixed.