(since i cant just say thank you and i have to enter more text to submit my thank you i had to write this essay to be able to press on the "post quick reply, please disregard this text below. Thank you , have a great day)
If I remember correctly (I read it on php.net somewhere) the manual at least uses SQLite for performance reasons. An educated guess would lead me along the lines of thinking that perhaps they also use that for their 'main site'.
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__________________ Programmers are in a race with the Universe to create bigger and better idiot-proof programs, while the Universe is trying to create bigger and better idiots. So far the Universe is winning. - Rich Cook
Reading those articles it sounds more like stupid administrators than an actual exploit. Couple of the articles on this have been saying it sounds like ssh passwords have been figured out and that's how they are getting in. Stupid administrators using simple passwords for users or not changing them from their default setting.