I have did some reading on "Merging Makefiles", one suggest I should leave the two Makefiles separate in different folders [1]. For me this look counter intuitive, because I have the following situation:

I have 3 source files (main.cpp flexibility.cpp constraints.cpp) one of them (flexibility.cpp) is making use of the COIN-OR Linear Programming library (Clp) When installing this library on my computer it makes sample Makefiles, which I have adjust the Makefile and it currently makes a good working binary.

# Copyright (C) 2006 International Business Machines and others.
# All Rights Reserved.
# This file is distributed under the Eclipse Public License.

# $Id: Makefile.in 726 2006-04-17 04:16:00Z andreasw $

##########################################################################
#    You can modify this example makefile to fit for your own program.   #
#    Usually, you only need to change the five CHANGEME entries below.   #
##########################################################################

# To compile other examples, either changed the following line, or
# add the argument DRIVER=problem_name to make
DRIVER = main

# CHANGEME: This should be the name of your executable
EXE = clp

# CHANGEME: Here is the name of all object files corresponding to the source
#           code that you wrote in order to define the problem statement
OBJS =  $(DRIVER).o constraints.o flexibility.o

# CHANGEME: Additional libraries
ADDLIBS =

# CHANGEME: Additional flags for compilation (e.g., include flags)
ADDINCFLAGS =

# CHANGEME: Directory to the sources for the (example) problem definition
# files
SRCDIR = .


##########################################################################
#  Usually, you don't have to change anything below.  Note that if you   #
#  change certain compiler options, you might have to recompile the      #
#  COIN package.                                                         #
##########################################################################

COIN_HAS_PKGCONFIG = TRUE
COIN_CXX_IS_CL = #TRUE
COIN_HAS_SAMPLE = TRUE
COIN_HAS_NETLIB = #TRUE

# C++ Compiler command
CXX = g++

# C++ Compiler options
CXXFLAGS = -O3 -pipe -DNDEBUG -pedantic-errors -Wparentheses -Wreturn-type -Wcast-qual -Wall -Wpointer-arith -Wwrite-strings -Wconversion -Wno-unknown-pragmas -Wno-long-long   -DCLP_BUILD

# additional C++ Compiler options for linking
CXXLINKFLAGS =  -Wl,--rpath -Wl,/home/martijn/Downloads/COIN/coin-Clp/lib

# C Compiler command
CC = gcc

# C Compiler options
CFLAGS = -O3 -pipe -DNDEBUG -pedantic-errors -Wimplicit -Wparentheses -Wsequence-point -Wreturn-type -Wcast-qual -Wall -Wno-unknown-pragmas -Wno-long-long   -DCLP_BUILD

# Sample data directory
ifeq ($(COIN_HAS_SAMPLE), TRUE)
  ifeq ($(COIN_HAS_PKGCONFIG), TRUE)
    CXXFLAGS += -DSAMPLEDIR=\"`PKG_CONFIG_PATH=/home/martijn/Downloads/COIN/coin-Clp/lib64/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/lib/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/share/pkgconfig: pkg-config --variable=datadir coindatasample`\"
      CFLAGS += -DSAMPLEDIR=\"`PKG_CONFIG_PATH=/home/martijn/Downloads/COIN/coin-Clp/lib64/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/lib/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/share/pkgconfig: pkg-config --variable=datadir coindatasample`\"
  else
    CXXFLAGS += -DSAMPLEDIR=\"\"
      CFLAGS += -DSAMPLEDIR=\"\"
  endif
endif

# Netlib data directory
ifeq ($(COIN_HAS_NETLIB), TRUE)
  ifeq ($(COIN_HAS_PKGCONFIG), TRUE)
    CXXFLAGS += -DNETLIBDIR=\"`PKG_CONFIG_PATH=/home/martijn/Downloads/COIN/coin-Clp/lib64/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/lib/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/share/pkgconfig: pkg-config --variable=datadir coindatanetlib`\"
      CFLAGS += -DNETLIBDIR=\"`PKG_CONFIG_PATH=/home/martijn/Downloads/COIN/coin-Clp/lib64/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/lib/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/share/pkgconfig: pkg-config --variable=datadir coindatanetlib`\"
  else
    CXXFLAGS += -DNETLIBDIR=\"\"
      CFLAGS += -DNETLIBDIR=\"\"
  endif
endif

# Include directories (we use the CYGPATH_W variables to allow compilation with Windows compilers)
ifeq ($(COIN_HAS_PKGCONFIG), TRUE)
  INCL = `PKG_CONFIG_PATH=/home/martijn/Downloads/COIN/coin-Clp/lib64/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/lib/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/share/pkgconfig: pkg-config --cflags clp`
else
  INCL = 
endif
INCL += $(ADDINCFLAGS)

# Linker flags
ifeq ($(COIN_HAS_PKGCONFIG), TRUE)
  LIBS = `PKG_CONFIG_PATH=/home/martijn/Downloads/COIN/coin-Clp/lib64/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/lib/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/share/pkgconfig: pkg-config --libs clp`
else
  ifeq ($(COIN_CXX_IS_CL), TRUE)
    LIBS = -link -libpath:`$(CYGPATH_W) /home/martijn/Downloads/COIN/coin-Clp/lib` libClp.lib 
  else
    LIBS = -L/home/martijn/Downloads/COIN/coin-Clp/lib -lClp 
  endif
endif

# The following is necessary under cygwin, if native compilers are used
CYGPATH_W = echo

# Here we list all possible generated objects or executables to delete them
CLEANFILES = clp \
    main.o \
    flexibility.o \
    constraints.o \

all: $(EXE)

.SUFFIXES: .cpp .c .o .obj

$(EXE): $(OBJS)
    bla=;\
    for file in $(OBJS); do bla="$$bla `$(CYGPATH_W) $$file`"; done; \
    $(CXX) $(CXXLINKFLAGS) $(CXXFLAGS) -o $@ $$bla $(LIBS) $(ADDLIBS)

clean:
    rm -rf $(CLEANFILES)

.cpp.o:
    $(CXX) $(CXXFLAGS) $(INCL) -c -o $@ `test -f '$<' || echo '$(SRCDIR)/'`$<


.cpp.obj:
    $(CXX) $(CXXFLAGS) $(INCL) -c -o $@ `if test -f '$<'; then $(CYGPATH_W) '$<'; else $(CYGPATH_W) '$(SRCDIR)/$<'; fi`

.c.o:
    $(CC) $(CFLAGS) $(INCL) -c -o $@ `test -f '$<' || echo '$(SRCDIR)/'`$<


.c.obj:
    $(CC) $(CFLAGS) $(INCL) -c -o $@ `if test -f '$<'; then $(CYGPATH_W) '$<'; else $(CYGPATH_W) '$(SRCDIR)/$<'; fi`

The other Makefile compiles a lot of code and makes use of bison and flex. This one is also made by someone else. I am able to alter this Makefile when I want to add some code. This Makefile also makes a binary.

CFLAGS=-Wall
LDLIBS=-LC:/GnuWin32/lib -lfl -lm
LSOURCES=lex.l
YSOURCES=grammar.ypp
CSOURCES=debug.cpp esta_plus.cpp heap.cpp main.cpp stjn.cpp timing.cpp tmsp.cpp token.cpp chaining.cpp flexibility.cpp exceptions.cpp
HSOURCES=$(CSOURCES:.cpp=.h) includes.h
OBJECTS=$(LSOURCES:.l=.o) $(YSOURCES:.ypp=.tab.o) $(CSOURCES:.cpp=.o)

all: solver

solver: CFLAGS+=-g -O0 -DDEBUG
solver: $(OBJECTS) main.o debug.o
    g++ $(CFLAGS) -o $@ $^ $(LDLIBS)

solver.release: CFLAGS+=-O5
solver.release: $(OBJECTS) main.o
    g++ $(CFLAGS) -o $@ $^ $(LDLIBS)

%.o: %.cpp
    g++ -c $(CFLAGS) -o $@ $<

lex.cpp: lex.l grammar.tab.cpp grammar.tab.hpp
    flex -o$@ $<

%.tab.cpp %.tab.hpp: %.ypp
    bison --verbose -d $<

ifneq ($(LSOURCES),)
$(LSOURCES:.l=.cpp): $(YSOURCES:.y=.tab.h)
endif

-include $(OBJECTS:.o=.d)

clean:
    rm -f $(OBJECTS) $(OBJECTS:.o=.d) $(YSOURCES:.ypp=.tab.cpp) $(YSOURCES:.ypp=.tab.hpp) $(YSOURCES:.ypp=.output) $(LSOURCES:.l=.cpp) solver solver.release 2>/dev/null

.PHONY: all clean debug release

Both of these Makefiles are, for me, hard to understand. I don't know what they exactly do. What I want is to merge the two of them so I get only one binary. The code compiled in the second Makefile should be the result. I want to add flexibility.cpp and constraints.cpp to the second Makefile, but when I do. I get the problem following problem:

flexibility.h:4:26: fatal error: ClpSimplex.hpp: No such file or directory
#include "ClpSimplex.hpp"

So the compiler can't find the Clp library. I also tried to copy-paste more code from the first Makefile into the second, but it still gives me that same error.

Q: Can you please help me with merging the two makefiles or pointing out a more elegant way?
Q: In this case is it indeed better to merge the two Makefiles?

I also tried to use cmake, but I gave upon that one quickly, because I don't know much about flex and bison.