In my case, I use NetBeans IDE to compile the daemon remotely on the Zynthian itself (but I think you can use directly the makefile from CLI, as NetBeans simply upload them and launch them remotely)
I have found the Makefile (I don’t know why it eluded me before) but it fails because it looks for ../../../../../SDK/beb/common_src/CThread.cpp which takes it beyond the root directory! I cloned the three repos into the root home directory on the zynthian and run make from command line whilst within the jacknetumpd/jacknetumpd directory.
I will try to create a makefile tomorrow. On your side, maybe you can ask to @jofemodo how he deals with the compilation for the Zynthian (as far as I know, he compiles the daemon locally, and does not use the compiled binary available on my Git)