The starting html file for the MTEXdoc command can be found in doc/html/mtex_product_page.html. When you use matlab help you can see in the lower toolbar the path of the html link by hovering the cursor above it (see attached picture).
Each help file in the doc/html folder can be produced by publishing a matlab file (.m) with the same name in the doc folder. For example, if you want the pdf version of the doc/html/GrainReconstructionDemo.html (Grains 'First Steps and Function Overview') you can open doc/GrainAnalyses/GrainReconstructionDemo.m and publish the file as pdf (or doc, html, etc.).
Cheers,
Filippe
