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Dealing with a trojan virus on dreamhost

I host a lot of simple sites on Dreamhost.  Imagine my surprise when I went to log into my control panel and was informed that google had listed one of my sites as being a suspected malware site.

The site that it referenced was a very rarely used site, that only housed a custom built app (more of a script than an actual app) so I was puzzled as to how this site could have become infected.

I logged into the host, and did a quick check of the directory structure, and immediately noticed some suspicious things. Read the rest of this entry »