You have requested document class X but the document class provides Y warning

This stems from the fact that you have PhDThesisPSnPDF.cls inside a Classes subfolder. So, the way you normally include it is to use

\documentclass[..]{Classes/PhDThesisPSnPDF}

right? Well, there should be similarity between what is supplied within \documentclass's mandatory argument - the class - and what is written inside the mandatory argument of \ProvidesClass inside PhDThesisPSnPDF.cls. If they don't match, LaTeX throws the warning you see.

You can't use the silence package for this unless you load it before calling \documentclass. Moreover, you don't have to supply the full warning message in order to filter it; just a matching start would do.

How can you rectify this warning? One of a number of ways:

1. Edit the PhDThesisPSnPDF.cls file inside the Classes subfolder and change

   \ProvidesClass{PhDThesisPSnPDF}
   

   to

   \ProvidesClass{Classes/PhDThesisPSnPDF}
   

   and then directly use

   \documentclass[..]{Classes/PhDThesisPSnPDF}
   

   inside your document.

2. Move PhDThesisPSnPDF.cls from the Classes folder to where you have your .tex source.

3. Move PhDThesisPSnPDF.cls to your local TeXMF folder and rerun texhash (making it available for all documents).

The following is directly from the templates README file:

Troubleshooting warnings

W1: I get the LaTeX Warning: You have requested document class Classes/PhDThesisPSnPDF, but the document class provides PhDThesisPSnPDF, should I be concerned?

No! Do nothing, or if you don't want any warning messages change the line near the top of the class file to \ProvidesClass{Classes/PhDthesisPSnPDF} if you're not going to install the class file in a more standard location. You can install it in a standard location like /usr/share/texmf/tex/latex/ and run texhash to reconfigure.

Please see also issue 112