There currently are concurrency issues in the order dependencies are defined and used, and cpu dependencies cannot be easily parsed.

I plan to address this by moving the processing of Makefile.dep before including $(BOARD)/Makefile.include

Dependencies resolution uses the following variables

• USEMODULE
• USEPKG
• FEATURES_
• BOARD
• CPU
• CPU_FAM (which depend on files in CPU)
• CPU_ARCH (which depend on files in CPU)
• CPU_MODEL

Steps

• Fix CPU dependencies not being parsed easily as reported first in Makefile.dep: process cpu dependencies and fix stm32_common #9892
  • Add a new file in board that include the common files too and currently only defines CPU, Makefile.board. Reuse Makefile.features to define CPU
  • Migration of CPU/CPU_MODEL Tracking: move CPU/CPU_MODEL to Makefile.features #11477
    • Makefile.features: assert CPU is defined by BOARD/Makefile.features Makefile.features: assert CPU is defined by BOARD/Makefile.features #12417
  • Move CPU dependencies to $(CPU)/Makefile.dep
  • Fix the stm32_common issue described in Makefile.dep: process cpu dependencies and fix stm32_common #9892
    • Remove them being defined as dependencies cpu/stm32_common: fix source selection declared as module dependencies (broken) #10153
• At that point, Makefile.features can be split to directly do include $(RIOTCPU)/$(CPU)/Makefile.features instead of hardwriting it.
• Fix CPU_FAM and CPU_ARCH defined in Makefile.include when they should be already available for Makefile.dep. Define them in Makefile.cpu Makefile.features files.
• doc: document how to handle multiple cpu_models in a directory doc: document how to handle multiple cpu_models in a directory #12407
• Move all BOARD/CPU dependencies to $(BOARD)/Makefile.dep and $(CPU)/Makefile.dep
• Fix other USEMODULE defined in Makefile.include issues (can be done in parallel)
  • USEMODULE += $(SKETCH_MODULE) /sys/arduino/Makefile.include
• Move Makefile.dep before doing Makefile.include. Makefile.include: resolve dependencies before Makefile.include #14351
• Reorganize files inclusion to be done only when needed

Prerequisites cleanup

• mips-malta including common cpu features board/mips-malta: include the cpu features instead of common cpu #10064
• boards: always include cpu features boards: always include cpu features #10078
  • cpu/esp8266 re-defining CPU cpu/esp8266: remove duplicate 'CPU' variable #10061
  • hifive1 not processing CPU features boards/hifive1: include cpu/fe310 features #10063
• cpu/fe310: rtc depend on the rtt feature and hifive1 update cpu/fe310: rtc depend on the rtt feature and hifive1 update #10062
• static_tests: add build system checks static_tests: add build system checks #10060

And even future improvement to remove multiple duplication between board/board_common cpu/cpu_common path:

• With BOARD and CPU recursively including their Makefile.board and Makefile.cpu, define some BOARD_IMPLEMENTATION_DIRS like variables that can be re-used to remove duplication in Makefile, Makefile.deps, Makefile.include, Makefile.features.

Explanation

To summarize, the main Makefile.include does regarding modules:
(a more detailed version is available here https://gist.github.com/cladmi/1c5af63c753635b7cb173cf8311d0b5b)

include $(RIOTBOARD)/$(BOARD)/Makefile.features
    # Define FEATURES_PROVIDED
    # Include with hard written path CPU/Makefile.features

include $(RIOTBOARD)/$(BOARD)/Makefile.include
    # Defines CPU
    # Defines USEMODULE
    # Have specific behavior depending on USEMODULE/USEPKG
include $(RIOTBOARD)/$(CPU)/Makefile.include
    # Define USEMODULE
    # Have specific behavior depending on USEMODULE/USEPKG
    # Define module dependencies

include Makefile.dep
    # Resolve USEMODULE/USEPKG/FEATURES_USED using:
    # * USEMODULE
    # * USEPKG
    # * FEATURES_
    # * BOARD
    # * CPU
    # * CPU_FAM
    # * CPU_ARCH 

include $(RIOTBASE)/sys/Makefile.include
include $(RIOTBASE)/drivers/Makefile.include
-include $(USEPKG:%=$(RIOTPKG)/%/Makefile.include)
include $(RIOTMAKE)/bindist.inc.mk
    # These also add things to USEMODULE

The main Makefile.dep only includes $(BOARD)/Makefile.dep which may sometime also end up including hardwritten_cpu_name/Makefile.dep.

In the same time makefiles/info-global.inc.mk does:

include $(RIOTBOARD)/$(BOARD)/Makefile.features
include $(RIOTBASE)/Makefile.dep

And so never takes into account any of the dependencies defined in $(BOARD)/Makefile.include or any other Makeflie.include files.