Fixed in r3380.

The cause of the problem was that gcc -MM strips the directory part of the
target file in the rules it generates. From "man gcc" (section on -M):

           Unless specified explicitly (with -MT or -MQ), the object file name
           consists of the name of the source file with any suffix replaced
           with object file suffix and with any leading directory parts
           removed.

The trunk Makefile doesn't track dependencies for code in subdirectories.

For example, Makefile.depend contains the following entry:

obj/landmarks_graph.o: landmarks/landmarks_graph.cc \
  landmarks/landmarks_graph.h landmarks/../operator.h \
  landmarks/../globals.h landmarks/../state.h landmarks/exploration.h \
  landmarks/../heuristic.h landmarks/../globals.h \
  landmarks/landmarks_types.h landmarks/../state.h landmarks/util.h

This is wrong: the target at the start should be obj/landmarks/landmarks_graph.o.