Paul Reinheimer has a recent post to his blog talking about the danger of "hooks" in your development - the functionality several frameworks and other tools come with to allow you to add functionality to the core without having to change the main source.
I ran into hooks rather simultaneously with two very different frameworks: Code Igniter and Lithium. In both cases I was using a rather nifty hook to handle ensuring that users were properly authenticated and authorized before accessing a page. [...] One day, while messing around, I accidentally turned off the hook configuration within Code Igniter (actually I clobbered a file, and restored the wrong one). Then, things came crashing down in a horrible cacophony of... actually they didn't. Everything kept working: that was the problem.
He shows two solutions he came up with to be sure that his hooks were executed - one for Lithium and the other for CodeIgniter. The Lithium one uses a "_remap" method and the CodeIgniter example uses the magic "__invoke" method to check for an "AUTH_CHECKED" constant that's only defined as a part of his hooks.
I'm no longer entirely dependent on one configuration option or file for my security to function. Should it fail, I've got a secondary check in place; this example of defence in depth allows me to be comfortable with the hooks security system once more.