Ok, so the problem seems to be with the makefile in the viewer subdirectory- for whatever reason, whatever the first entry in the SOURCES variable is will not compile:
SOURCES = \
d2layer.cc \
d3layer.cc \
decorationlayer.cc \
exportlayer.cc \
imagelayer.cc \
latticelayer.cc \
layer.cc \
nox.cc \
palettelayer.cc \
userdumplayer.cc \
usrbinlayer.cc \
viewer.cc \
voxellayer.cc \
i.e. if I change the positions of d3layer.cc and d2layer.cc, the compiler can find d2layer.cc but not d3layer.cc. If I put some other file at the top of the list, it’s the same problem with whatever file I put there. I’ve checked for leading/trailing whitespaces- doesn’t seem that there is any. But basically there’s some problem with how the makefile is processing the SOURCES variable.