Hi,
First of all, please check that the flags.mak has been saved and successfully deployed to the Linux machine. If it has been deployed, double-check the Makefile. The following lines are responsible for using INCLUDE_DIRS:
CFLAGS += $(addprefix -I,$(INCLUDE_DIRS))
CXXFLAGS += $(addprefix -I,$(INCLUDE_DIRS))
...
$(BINARYDIR)/%.o : %.cpp $(all_make_files) |$(BINARYDIR)
$(CXX) $(CXXFLAGS) -c $< -o $@ -MD -MF $(@:.o=.dep)
If the Makefile looks correct, but INCLUDE_DIRS is still ignored, you can experiment with it by modifying CXXFLAGS/INCLUDE_DIRS directly from the Makefile. If overriding the value at some line has no effect, most likely it is overridden somewhere after that line.