Add support for manually modified kernel headers.

This changes the scripts so that if some kernel files exists
in external/kernel-headers/modified, that they will be preferred
over the same files found in original. This is to support the case
where the kernel headers cannot be taken without some small modifications.

Included with this change, is a general cleanup of the python scripts.

This also modifies the generate uapi headers script to indicate if the
source of the modified headers has changed.

Change-Id: Id13523b244ced52a2ecd9f1399c43996dd8296fa