[SOLVED] Why I Hate Upgrading Atahualpa

Why is it that every time I install an upgrade of the theme, it has overwritten my custom header and the like. If it is necessary to replace all the files in the theme directory, please make it possible for me to place my headers, logos, etc... in a location that will not be affected by an update.

I use Atahualpa on a number of web-sites - both personal and client sites - and every time I see that there is an update I am both excited and filled with dread.