samples: usb: dfu: Fix building of dfu code

We've transitioned to use $ZEPHYR_BASE instead of srctree due to how we
might invoke the kbuild system.  Change include paths to be $ZEPHYR_BASE
relative instead of $srctree.

Change-Id: Ib7428a1821a81a4537c6d5d98ee91e30f0cce435
Signed-off-by: Kumar Gala <kumar.gala@linaro.org>