I have been working on this server for the entire semester and have not changed any configuration options - the directories/files I created a couple weeks ago are still accessible, however any new directories, even exact duplicate of old working directories don't let me access them - get error "Directory index forbidden by Options directive". What is causing this?
Looks like someone disabled directory listing in Apache. If you are allowed to override it with .htaccess just place an .htaccess file in your root web directory with this information:
Options +Indexes
For me this was an issue with not simply having an index.html or index.php (depending on what is in the .htaccess file) file in a folder and trying to pull it's contents. Then again I was using php to read contents, not by command line like I assume you are. If you still have not found a solution try creating an index.(php,html) in the directory that you can't pull contents from.
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