The Scrybe plugin for phpDocumentor allows you to generate manuals and other hand-made reference materials by combining a markup language and a template. Currently this plugin can generate HTML documentation but support for PDF and LaTeX is planned.
To use this plugin, all you need to do is invoke the correct command::
$ ./bin/phpdoc manual:to-html -t build/docs src
The above command will generate HTML documentation from the markup files in the src folder into the build/docs
folder.