apply-patches.sh: directories are no more considered as overlays

When a directory is found in patchdir, it is skipped.

Signed-off-by: Ludovic Desroches <ludovic.desroches@atmel.com>
Tested-by: Ludovic Desroches <ludovic.desroches@atmel.com>
with an armadeus_apf9328_defconfig build
Acked-by: Thomas Petazzoni <thomas.petazzoni@free-electrons.com>
Tested-by: Thomas Petazzoni <thomas.petazzoni@free-electrons.com>
Signed-off-by: Peter Korsgaard <jacmet@sunsite.dk>