Additional to defining PROJECTROOT and THISDIR, every Makefile in a subdirectory should also list the .nw files and subdirectories in its respective directory. The variables FILES and DIRS are used for this purpose.
An exception are the Aldor source files. Their names should be listed in myalps.tex.nw (projectname.tex). During a submake call (Section 29.3) these names will be extracted and written (in the form of a variables assignment to the variable ASFILES) to Makefile.asfiles in the corresponding subdirectories as given by DIRS, in particular to src/Makefile.asfiles and test/Makefile.asfiles
Additional directories can be given in Makefile.def.nw through the variable ADDITIONALTOPLEVELDIRS, see Section 15.3.