SOSTX

One of the backdoors to Moodle has been command line access/Webmin access to the data directory for the Moodle.  Contained therein in versions 1.9.x and lower were numbered directories which corresponded to the course ID's. To get large files which could NOT be uploaded due to restrictions in settings, one could copy a file to a location (course ID directory), change permissions so that apache user/group could see it, and the file was then available in the course.

In Moodle 2.0 that is no longer possible even if one of your repositories are local files. Moodle creates a filedir directory for local file repository now and contains varies folders created by Moodle.
Looks like:

[root@sos filedir]# ll
total 96
drwxrwxrwx 3 apache apache 4096 Mar 22 14:54 03
drwxrwxrwx 3 apache apache 4096 Mar 22 14:51 1f
drwxrwxrwx 3 apache apache 4096 Jun  7 09:54 53
drwxrwxrwx 3 apache apache 4096 Mar 22 14:49 63
drwxrwxrwx 3 apache apache 4096 Mar 22 15:02 a8
drwxrwxrwx 3 apache apache 4096 Mar 22 14:52 b0
drwxrwxrwx 3 apache apache 4096 Mar 22 15:01 c1
drwxrwxrwx 3 apache apache 4096 Mar 22 14:55 ce
drwxrwxrwx 3 apache apache 4096 Mar 22 14:49 da
drwxrwxrwx 3 apache apache 4096 Mar 22 15:04 e9
drwxrwxrwx 3 apache apache 4096 Mar 22 15:05 fa
-rw-rw-rw- 1 apache apache  168 Mar 22 14:16 warning.txt

The warning.txt file clearly states:
[root@sos filedir]# more warning.txt
This directory contains the content of uploaded files and is controlled by Moodle code. Do not manually move, change or rename any of the files and subdirectories here.

More emphasis will be placed on the database for controlling repositories now so backdoors to problems such as described might have to be explored by other means now.