Flex builder thinks all my files are "derived"

Whenever I start to modify any file in my flex application
(mxml, as), my flex builder pops up a warning saying "This file is
derived. Do you really want to edit it?"
This happens for code which I have written by hand, not
autogenerated. Anyone know what this is about?
-Raj

My Flex project settings had the same folder for both source
and output. Changing the output folder fixed the problem. It also
fixed another issue where my CSS files was being deleted
automatically.
Thanks a lot for your response.
-Raj

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