config: Only warn if duplicate option/device comes from the same file

This is useful for arm (possibly other arches too) where we want to have
a GENERIC kernel that only include files for the different SoC. Since
multiple SoCs/Board needs the same device we would need to do either :

Include the device in a generic file
Include the device in each file that really needs it

Option 1 works but if someone wants to create a specific kernel config
(which isn't uncommon for embedded system), he will need to add a lots
of nodevice to it.

Option 2 also works but produce a lots of warnings.

Reviewed by: kevans
MFC after: 2 weeks
Differential Revision: https://reviews.freebsd.org/D19424