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Last month, an OCS website I manage was attacked. A substantial chunk of the attack code was left in the /public/ directory. Any OCS developers wishing to have the code, please contact me.
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Review the discussion at http://pkp.sfu.ca/support/forum/viewtopic.php?f=8&t=3481
and see if that helps to identify the source of the problem. The problem could be lax file permissions, or an attack beginning in another application, or an attack targeting OCS -- but we haven't had any reports yet of vulnerabilities in OCS itself, so I'd start by looking at the first two options.
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