How do I go about applying a custom masterpage just to "front end" pages? i.e. I want all of the administration parts of the SharePoint site to follow default look and feel (viewlsts.aspx, managing lists and libraries, site settings etc) and then pages the standard user visits to have my custom branding.

What would I edit (masterpage, page layouts??) to add my extra CSS and JS files that will over-ride the default styles?

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Go to your site/_Layouts/ChangeSiteMasterPage.aspx and set the System master page as V4.master (I assume you're working in SP2010), to apply the default look and feel for pages like viewlsts.aspx, site settings and so on.

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