It could be due to the hundreds of baggage files in the project! And, I'm not technically adept enough to decipher scripting language. But, the baggage files are a necessary component at this point.
RoboHelp (WebHelp) creates .htm files. There is no native support for php in topics. You, as H says add all your php files as baggage files. The get brought into the output. You can call these pages using hyperlinks, and if I'm not mistaken open them from your table of contents.