package.bbclass: Fix various problems

Before this change:

a) Ownership and permissions of files copied from packages to
   package-split could get lost during the copy process. This change
   ensures they are preserved.
b) Ownership and permissions of directories could also get lost.
   Most of the complexity in this patch is addressing this problem
   ensuring newly created directories match the source ones being
   copied.
c) There was no warning about directories being created but not
   shipped by any package.

This patch fixes all of the above issues.

Signed-off-by: Richard Purdie <richard.purdie@linuxfoundation.org>

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