kvmtool: Makefile: replace kernel libfdt source with system library

kvmtool used the in-kernel version of the device tree handling
library. Now that we are a proper userland tool, use the system's
library for that purpose. Actually this seems to fix some
long-standing warning generated by the Linux copy.
Also fix up a bogus x86 warning (no FDT needed here).

Signed-off-by: Andre Przywara <andre.przywara@arm.com>