The solution to this was laughably simple.
all I had to do was touch CMakeLists.txt making a completely empty file in the zensekai directory, and then CMake automatically decided to continue in zensekai-click with the other CMakeLists.txt.

edit 7-13:
There was actually a little more required.

in the top CMakeLists.txt I had to put

add_subdirectory(zensekai-click)

and in the zensekai-click one I accessed/disambiguated the two directories with

# set $PR_ROOT to upper directory get_filename_component(PR_ROOT "../" ABSOLUTE) # set $CLICK_DIR to zensekai-click directory set(CLICK_DIR "${PR_ROOT}/zensekai-click")

another thing you might run into developing a click package that copies binaries is permissions on binaries.
I set them in the loop that copies the binaries like so:

foreach(binary ${BINARIES}) install(FILES ${PR_ROOT}/bin/${binary} # the important part PERMISSIONS OWNER_READ OWNER_EXECUTE GROUP_READ WORLD_READ WORLD_EXECUTE # this might actually be unnecessarily permissive*. # it might be enough to just have OWNER_READ and OWNER_EXECUTE DESTINATION ${DATA_DIR} ) endforeach()

(* I got sidetracked thinking the permissions weren't enough when I accidentally had my project copying the x86_64 godot binary for a bit - which had bash claiming it "wasn't permitted" to execute while it actually meant that was impossible.)

Just saw, someone (Jonny?) wrote an article on how to ship dependencies...
http://docs.ubports.com/de/latest/appdev/guides/dependencies.html