After being hit by the Wordpress base64 hack twice within a couple of weeks, it finally dawned me that the PHP CGI flaw was the culprit. The attack robots (a la Metasploit) use the knowledge of PGP CGI flaw together with the well-known scripts of popular products (Wordpress, Joomla, Drupal, etc.) to penetrate sites and that's how this site was breached as well.
Most sites run PHP as a module, so those were spared the headache. I used to run PHP as a module many moons ago, but chose to move to CGI for several reasons. Here's a an explanation of the difference between the two modes. What's disconcerting is that the CGI vulnerability had been around or some 8 years and no one seemed to have noticed during all that time and it was my PHP version 5.3.5 that did me in. It was time to move to version 5.3.14. But where to find that php-cgi version for my Fedora install.
I went hunting for php-cgi 5.3.14 all over the net, from user websites, to rpm repositories, but no dice for my Fedora version. Now sometimes you can use an off version, but then you run the risk of crashes, library mismatch and other problems. So why not download the source from php.net and build it myself? Simple, I'm too lazy and hate building/rebuilding programs. There's the big download, long waits, missing libraries, warnings and errors. I had just come off a build hell of Varnish cache, and I wasn't about to plunge myself into another. But, in the end I had no choice.
The Linux build world is a 3-word expression: configure, make, 'make install'. I'll add another word, loop. You download the source code, run configure to adjust the config and make files for your particular platform. Then you run make to build the program(s). finally you run 'make install' to install the program(s) on your system. Sounds easy enough until you realize that a million things can and will go wrong and that's where 'loop' comes in as you configure and make repeatedly to get things right.
Building PHP 5.3.14 didn't disappoint. I ended up running configure and make tens of times until I finally got the binary I wanted with all the necessary libraries included. Building php using make renders a number of binaries including the main command line program (interpreter) as well as php-cgi and it was the latter I was interest in.
I copied the newly-made php-cgi over the old version, tested the site and called it a day. Now I know this sort of installation is a cardinal sin to many techies, no argument there. Think about it, I am running a php-cgi version that is out of sync with the main php interpreter on the same machine and then the rpm (package manager) has no clue about which version of php is really installed on the system. At the first rpm update, the whole system could come crashing down. I just have to be cognizant of the fact that I have a fragmented php installation. Eventually when I migrate the site to a new Fedora version all will be back to good. For now, it's good enough to have been hack-free for a couple of months.