two CSS are being pulled from by index.php

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I put all content of catalog in root.
I left original catalog dir also in root.
It appears that some files are being used by index.php that are in the original catalog dir instead of using the files in the root.
IE: The stylesheet.css file
I kept making edits in the root copy of stylesheet.css with no results.
Editing the stylesheet.css inside the catalog dir made it happen.

Ok I thought - Just rename catalog to oldcatalog - solve problem.
Nope - made the store completely unusable.

I was told by one of the more experienced users here that to get my catalog to load when my url was accessed just put all contents of catalog into the root dir.

Obviously I do not need all files in root. In fact it appears that some of the files from the catalog will not work if in the root.

Anyone care to fill me in on the "which files need to be in the root" and "which files should NOT be in the root".

Thanks
Emmett