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answers:

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I have a file called webpart.cs which is called by one of my masterpages in Sharepoint, where are those files stored on the Server?

A: 

Assuming your master page is referencing a .css (and not a .cs) file, those are typically in /_catalogs/masterpage - but that entirely depends on the master page, and from HOW it's referencing the .css it should be fairly straightforward to figure out where the file lives.

There's no way of referencing a .cs file directly, you can reference the namespace and the assembly, but not the .cs file. Or are you talking about finding the .cs file that built the assembly ? If so, reflector is your friend if this isn't your assembly...

Rawbert