makefile with many source folders - linux

Question

The original makefile I have, which works, only involves one source folder and the makefile is stored inside this folder. Now I have multiple folders inside my src folder.
I am using an autogeneration script to work out dependencies and objective files. Each subfolder has a Make-deps and Make-objs file. These are generated from the $(AUTOGEN) command
Before I had this:
deps:
$(AUTOGEN) -d -s $(SRCDIR) -f ../scripts/fgenrc ;\
sed -i "" -e's/(SRCDIR)/(OBJDIR)/' Make-objs ; \
sed -i "" -e's/(SRCDIR)\(.*\)\.o/(OBJDIR)\1\.o/g' Make-deps ; \
So $(AUTOGEN) is just the shell script which makes the dependencies and $(SRCDIR) is where the source files are. Make-obj and Make-deps are the files containing the dependencies and objective file names.
Somewhere else I have the following:
$(OBJDIR)/%.o: %.f Makefile
#$(F90) $(FFLAGS) $(POPTIONS) -o $# $<
Now I want to this but where my %.f files are in various folders, and also where I have several Make-obj and Make-deps.
Maybe I should show an example of Make-obs and Make-deps:
Make-deps:
$(OBJDIR)/fluxes.o fluxes.o: \
path/to/src/folder1/fluxes.f90 \
$(OBJDIR)/mod.o \
$(OBJDIR)/ig.o ig.o: \
path/to/src/folder1/ig.f90 \
$(OBJDIR)/mod.o \
from the sed command I change the objective file path to be $(OBJDIR) because this is where I move them when being compiled.
Make-obj
OBJS = \
$(OBJDIR)/fluxes.o \
$(OBJDIR)/ig.o \
Now I have defined
SOURCE_FILES_c := $(shell find $(SRCDIR) -name '*.c')
SOURCE_FILES_f90 := $(shell find $(SRCDIR) -name '*.f90')
which are all source files found the SRCDIR and its subfolders. Also I have defined
DEPS_FILES := $(shell find $(SRCDIR) -name 'Makefile-deps')
OBJS_FILES := $(shell find $(SRCDIR) -name 'Makefile-objs')
which are all dependency and objective files. These are found in each subfolder containing some source code.
Then, I am trying to do following. (The target deps seems to work as when I comment out the compilation rule it does create the deps and objs file correctly in each folder.)
code: create_dir deps scripts
#make -j $(CORES) $(NAMEEXE)
$(NAMEEXE): $(LIBRARY) $(OBJS)
#$(F90) $(FFLAGS) $(OPTIONS) -o $(OBJDIR)/$(MAIN).o main/$(MAIN).f90
#$(F90) -o $(NAMEEXE) $(LOPTIONS) $(OBJS) $(LIBRARY) && \
deps:
${AUTOGEN} -d $(AUTOGEN_COMMAND) -f ${AUTOCONF} ; \
$(SEDI) -e "s/[(][^)]*[)]/\$$(OBJDIR)/g" $(OBJS_FILES) ; \
$(SEDI) -e "s/[(][^)]*[)]\(.*\)\.o/\$$(OBJDIR)\1\.o/g"
$(DEPS_FILES) ; \
$(OBJDIR)/%.o: $(SOURCE_FILES_f:.f90=.o) Makefile
#$(F90) $(FFLAGS) $(POPTIONS) -o $# $< && \
( mv -f *.mod $(OBJDIR) > /dev/null 2>&1;
$(OBJDIR)/%.o: $(SOURCE_FILES_c:.c=.o) Makefile
#$(F90) $(FFLAGS) $(POPTIONS) -o $# $< && \
( mv -f *.mod $(OBJDIR) > /dev/null 2>&1;
%.o: $(SOURCE_FILES_c:.c=.o) Makefile
#make $(OBJDIR)/$#
%.o: $(SOURCE_FILES_c:.c=.f90) Makefile
#make $(OBJDIR)/$#
I am including the deps and objs by this command
-include $(DEPS_FILES)
-include $(OBJS_FILES)
I obviously did not want put the entire makefile here, but if something is missing before you can understand what's going on please let me know.
When I type make the error I get is that my $(main) source file cannot open the compiled module file which is included in the main source.
This is because it is not compiled, but this also means that my dependency file is not working as intended?
When I look into my corresponding dep file which includes the main file, I can see that the dependency modules are added to the source file