Area Customization (Including Home Area)

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I have done some minor customization of my portal areas, mainly
branding, and I was wondering if it is possible to point the areas at
custom definitions. When I did the customization, which consisted of
editing the aspx pages, I renamed the original files and created new
aspx pages. Now I want to copy all of the areas and create custom
definitions but I understand Microsoft "doesn't support" changing
existing areas. Basically what I would like to do is create custom
areas for all areas (including the home area) and then point the areas
to the new custom definitions. All of this so when I update Portal/WSS
I do not overwrite my branding. Can this be done? Can I do this
manually or should I do it using the Object Model?

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