In a quick post to his blog Hasan Otuome points out an issue he had when running phpDocumentor on his application's codebase resulting in a broken end result.

Recently had to run PhpDocumentor on a project only to be faced with broken documentation after bringing all class files into compliance with proper comments. At first I thought I was missing a config flag for the command-line but, it turns out that the PhpDocumentor-1.4.3 ZIP download contains broken template elements.

He provides two screenshots showing the broken result of his run (wrong extensions mainly) and how he used this tool to correct the damage.