This stems from the fact that you have
PhDThesisPSnPDF.cls inside a
Classes subfolder. So, the way you normally include it is to use
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
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:
PhDThesisPSnPDF.cls file inside the
Classes subfolder and change
and then directly use
inside your document.
PhDThesisPSnPDF.cls from the
Classes folder to where you have your
PhDThesisPSnPDF.cls to your local TeXMF folder and rerun
texhash (making it available for all documents).