The work directory is an automatically-generated component of the RUN directory. Early on in the assembly process, it does not exist, but eventually it will contain the output of pre-processing and the SUBDIRs.
From the user's point of view, the upshot is very simple. When you initially run a script module such as Assemble or Assemblez, you should specify RUN without work. For example, if you put RUN=run, Assemblez will create run and put several useful output files there; it will also create run/work and put more files there. After Assemblez is done, all further assembly modules and post-processing modules should give RUN=run/work.