make: Rename all included files to `Makefile.mk`

[crawfxrd]

Standardize the Makefiles to use a single name.

Done with:

find . -name *.mk -not -path '*/toolchain.mk' -execdir mv {} Makefile.mk \;
grep -rl common.mk src/ | xargs sed -i 's/common.mk/Makefile.mk/'
grep -rl keyboard.mk src/ | xargs sed -i 's/keyboard.mk/Makefile.mk/'
grep -rl scratch.mk src/ | xargs sed -i 's/scratch.mk/Makefile.mk/'
grep -rl flash.mk src/ | xargs sed -i 's/flash.mk/Makefile.mk/'