I'm sorry that this happened; it's really not as easy as most people think it is to lock down a server. I've had many a times where my server logs go crazy with people random-guessing my SSH logins or trying to exploit upload systems.
I do applaud the move away from MSI/EXE installers though. This will certainly help the aftermath and pretty much eliminate the problem.
A thought though; perhaps it would be wise for Blizzard to include a module installation system where developers can simply package a file up in a self-contained (NOT executable) file, ie: someMod.wowadd, and a program Blizzard provides would extract/place the files where they need to go. This is similar to what the Unreal engine does with UMOD's, etc, and it works out really well.
<3
-Cid
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