I thought I was being smart, I wanted to download some Debian packages so I went to /var/cache/apt/archives and did "rm -rf *" but then I couldn't use apt-get anymore. I kept getting this error:
E: Archive directory /var/cache/apt/archives/partial is missing.
E: The list of sources could not be read.
The solution was to recreate the "partial" directory inside /var/cache/apt/archives and then everything will be fine.