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Have you tried purging rosdep and installing it again?

Could you paste the permissions from that directory an its files on your system? Maybe they are really not listable resp. readable for everyone.

This is how it looks on mine:

$ ll /etc/ros/rosdep/sources.list.d
total 12
drwxr-xr-x 2 root root 4096 2012-03-16 11:41 ./
drwxr-xr-x 3 root root 4096 2012-03-16 11:41 ../
-rw-r--r-- 1 root root  409 2012-03-16 11:41 20-default.list

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