Rick's response prompts me to suggest another possibility. You could create a file system repository to upload the files into. Then you can essentially create your own manageable structure and link to those files from the courses.
Hi Bret,
I'm looking into this. If there's a plugin which reads file system structure from a location and displays is as a file tree in Moodle. On clicking on each member of tree the content gets displayed on the right side of the file tree in Moodle??
There is a JavaScript and php plugin available for file tree structure but I don't know how to make it communicate with Moodle.
While I use the file system repository, I don't use it heavily enough to require a tree structure on the left side. Only the repository name is shown there. Subfolders are shown on the right side, which I guess if you had hundreds of them would be a bit messy. Sorry, I haven't researched whether there is a plugin to adjust that behavior.