I added $(srctree)/ to some included Makefiles in the following commits:
 - 
3204a7fb98a3 ("kbuild: prefix $(srctree)/ to some included Makefiles")
 - 
d82856395505 ("kbuild: do not require sub-make for separate output tree builds")
They were a preparation for removing --include-dir flag.
I have never thought --include-dir useful. Rather, it _is_ harmful.
For example, run the following commands:
  $ make -s ARCH=x86 mrproper defconfig
  $ make ARCH=arm O=foo dtbs
  make[1]: Entering directory '/tmp/linux/foo'
    HOSTCC  scripts/basic/fixdep
  Error: kernelrelease not valid - run 'make prepare' to update it
    UPD     include/config/kernel.release
  make[1]: Leaving directory '/tmp/linux/foo'
The first command configures the source tree for x86. The next command
tries to build ARM device trees in the separate foo/ directory - this
must stop because the directory foo/ has not been configured yet.
However, due to --include-dir=$(abs_srctree), the top Makefile includes
the wrong include/config/auto.conf from the source tree and continues
building. Kbuild traverses the directory tree, but of course it does
not work correctly. The Error message is also pointless - 'make prepare'
does not help at all for fixing the issue.
This commit fixes more arch Makefile, and finally removes --include-dir
from the top Makefile.
There are more breakages under drivers/, but I do not volunteer to fix
them all. I just moved --include-dir to drivers/Makefile.
With this commit, the second command will stop with a sensible message.
  $ make -s ARCH=x86 mrproper defconfig
  $ make ARCH=arm O=foo dtbs
  make[1]: Entering directory '/tmp/linux/foo'
    SYNC    include/config/auto.conf.cmd
  ***
  *** The source tree is not clean, please run 'make ARCH=arm mrproper'
  *** in /tmp/linux
  ***
  make[2]: *** [../Makefile:646: outputmakefile] Error 1
  /tmp/linux/Makefile:770: include/config/auto.conf.cmd: No such file or directory
  make[1]: *** [/tmp/linux/Makefile:793: include/config/auto.conf.cmd] Error 2
  make[1]: Leaving directory '/tmp/linux/foo'
  make: *** [Makefile:226: __sub-make] Error 2
Signed-off-by: Masahiro Yamada <masahiroy@kernel.org>
 $(error source directory cannot contain spaces or colons)
 endif
 
-ifneq ($(abs_srctree),$(abs_objtree))
-# Look for make include files relative to root of kernel src
-#
-# --included-dir is added for backward compatibility, but you should not rely on
-# it. Please add $(srctree)/ prefix to include Makefiles in the source tree.
-MAKEFLAGS += --include-dir=$(abs_srctree)
-endif
-
 ifneq ($(filter 3.%,$(MAKE_VERSION)),)
 # 'MAKEFLAGS += -rR' does not immediately become effective for GNU Make 3.x
 # We need to invoke sub-make to avoid implicit rules in the top Makefile.
 
 # Copyright 2009 Simtec Electronics
 
 ifdef CONFIG_ARCH_S3C24XX
-include $(src)/Makefile.s3c24xx
+include $(srctree)/$(src)/Makefile.s3c24xx
 endif
 
 ifdef CONFIG_ARCH_S3C64XX
-include $(src)/Makefile.s3c64xx
+include $(srctree)/$(src)/Makefile.s3c64xx
 endif
 
 # Objects we always build independent of SoC choice
 
 CFLAGS_traps.o  += -mfixed-range=f2-f5,f16-f31
 
 # The gate DSO image is built using a special linker script.
-include $(src)/Makefile.gate
+include $(srctree)/$(src)/Makefile.gate
 
 endif
 
 # platform specific definitions
-include arch/mips/Kbuild.platforms
+include $(srctree)/arch/mips/Kbuild.platforms
 obj-y := $(platform-y)
 
 # make clean traverses $(obj-) without having included .config, so
 
 __archpost:
 
 -include include/config/auto.conf
-include scripts/Kbuild.include
+include $(srctree)/scripts/Kbuild.include
 
 CMD_LS3_LLSC = arch/mips/tools/loongson3-llsc-check
 quiet_cmd_ls3_llsc = LLSCCHK $@
 
 __archpost:
 
 -include include/config/auto.conf
-include scripts/Kbuild.include
+include $(srctree)/scripts/Kbuild.include
 
 quiet_cmd_head_check = CHKHEAD $@
       cmd_head_check = $(CONFIG_SHELL) $(srctree)/arch/powerpc/tools/head_check.sh "$(NM)" "$@"
 
 
 CFLAGS_xterm.o += '-DCONFIG_XTERM_CHAN_DEFAULT_EMULATOR="$(CONFIG_XTERM_CHAN_DEFAULT_EMULATOR)"'
 
-include arch/um/scripts/Makefile.rules
+include $(srctree)/arch/um/scripts/Makefile.rules
 
 
 USER_OBJS := config.o
 
-include arch/um/scripts/Makefile.rules
+include $(srctree)/arch/um/scripts/Makefile.rules
 
 targets := config.c config.tmp capflags.c
 
 
 
 KCOV_INSTRUMENT := n
 
-include arch/um/scripts/Makefile.rules
+include $(srctree)/arch/um/scripts/Makefile.rules
 
        main.o mem.o process.o registers.o sigio.o signal.o start_up.o time.o \
        tty.o umid.o util.o
 
-include arch/um/scripts/Makefile.rules
+include $(srctree)/arch/um/scripts/Makefile.rules
 
 obj-$(CONFIG_UML_NET_ETHERTAP) += ethertap.o
 obj-$(CONFIG_UML_NET_TUNTAP) += tuntap.o
 
-include arch/um/scripts/Makefile.rules
+include $(srctree)/arch/um/scripts/Makefile.rules
 
 
 USER_OBJS := $(obj-y)
 
-include arch/um/scripts/Makefile.rules
+include $(srctree)/arch/um/scripts/Makefile.rules
 
 export LDS_EXTRA
 
 # First of all, tune CFLAGS for the specific CPU. This actually sets cflags-y.
-include arch/x86/Makefile_32.cpu
+include $(srctree)/arch/x86/Makefile_32.cpu
 
 # prevent gcc from keeping the stack 16 byte aligned. Taken from i386.
 cflags-y += $(call cc-option,-mpreferred-stack-boundary=2)
 
 UNPROFILE_OBJS := stub_segv.o
 CFLAGS_stub_segv.o := $(CFLAGS_NO_HARDENING)
 
-include arch/um/scripts/Makefile.rules
+include $(srctree)/arch/um/scripts/Makefile.rules
 
 
 USER_OBJS := $(obj-y)
 
-include arch/um/scripts/Makefile.rules
+include $(srctree)/arch/um/scripts/Makefile.rules
 
 # Rewritten to use lists instead of if-statements.
 #
 
+# Some driver Makefiles miss $(srctree)/ for include directive.
+ifdef building_out_of_srctree
+MAKEFLAGS += --include-dir=$(srctree)
+endif
+
 obj-y                          += irqchip/
 obj-y                          += bus/
 
 
 obj-y :=
 obj-$(CONFIG_HOSTFS) += hostfs.o
 
-include arch/um/scripts/Makefile.rules
+include $(srctree)/arch/um/scripts/Makefile.rules