clean up all Makefiles:

- all objects now go in a dedicated dir
- to avoid error-prone repetitions, objects are put in env variables
- correct target mismatches that caused builds to be repeated even when not necessary

src/sphere/Makefile

-BUILDDIR=../../build/sphere
+ifndef BUILDDIR
+override BUILDDIR=../../build/sphere
+endif
+ifndef OBJDIR
+override OBJDIR=../objects
+endif
 
 include ../make.inc
 
-#FC=gfortran
-#FCFLAGS=-std=legacy -O3
-#LFLAGS=
-#CXX=g++
-#CXXFLAGS=-O2 -ggdb -pg -coverage
-#CXXLFLAGS=-L/usr/lib64 -lhdf5_hl -lhdf5
+F_SPH_OBJS=$(OBJDIR)/edfb_sph.o $(OBJDIR)/sph.o
 
-all: edfb_sph sph np_sphere
+CXX_SPH_OBJS=$(OBJDIR)/np_sphere.o $(OBJDIR)/Commons.o $(OBJDIR)/Configuration.o $(OBJDIR)/file_io.o $(OBJDIR)/Parsers.o $(OBJDIR)/sph_subs.o $(OBJDIR)/sphere.o
 
-edfb_sph: edfb_sph.o
-	$(FC) $(FCFLAGS) -o $(BUILDDIR)/edfb_sph $(BUILDDIR)/edfb_sph.o $(LDFLAGS)
 
-sph: sph.o
-	$(FC) $(FCFLAGS) -o $(BUILDDIR)/sph $(BUILDDIR)/sph.o $(LDFLAGS)
+all: $(BUILDDIR)/edfb_sph $(BUILDDIR)/sph $(BUILDDIR)/np_sphere
 
-np_sphere: $(BUILDDIR)/np_sphere.o $(BUILDDIR)/Commons.o $(BUILDDIR)/Configuration.o $(BUILDDIR)/file_io.o $(BUILDDIR)/Parsers.o $(BUILDDIR)/sph_subs.o $(BUILDDIR)/sphere.o
-	$(CXX) $(CXXFLAGS) -o $(BUILDDIR)/np_sphere $(BUILDDIR)/np_sphere.o $(BUILDDIR)/Commons.o $(BUILDDIR)/Configuration.o $(BUILDDIR)/file_io.o $(BUILDDIR)/Parsers.o $(BUILDDIR)/sph_subs.o $(BUILDDIR)/sphere.o $(CXXLDFLAGS) 
+$(BUILDDIR)/edfb_sph: $(OBJDIR)/edfb_sph.o
+	$(FC) $(FCFLAGS) -o $(BUILDDIR)/edfb_sph $(OBJDIR)/edfb_sph.o $(LDFLAGS)
 
-#$(BUILDDIR)/np_sphere.o:
-#	$(CXX) $(CXXFLAGS) -c np_sphere.cpp -o $(BUILDDIR)/np_sphere.o
+$(BUILDDIR)/sph: $(OBJDIR)/sph.o
+	$(FC) $(FCFLAGS) -o $(BUILDDIR)/sph $(OBJDIR)/sph.o $(LDFLAGS)
 
-#$(BUILDDIR)/Commons.o:
-#	$(CXX) $(CXXFLAGS) -c ../libnptm/Commons.cpp -o $(BUILDDIR)/Commons.o
-
-#$(BUILDDIR)/Configuration.o:
-#	$(CXX) $(CXXFLAGS) -c ../libnptm/Configuration.cpp -o $(BUILDDIR)/Configuration.o
-
-#$(BUILDDIR)/file_io.o:
-#	$(CXX) $(CXXFLAGS) -c ../libnptm/file_io.cpp -o $(BUILDDIR)/file_io.o
-
-#$(BUILDDIR)/Parsers.o:
-#	$(CXX) $(CXXFLAGS) -c ../libnptm/Parsers.cpp -o $(BUILDDIR)/Parsers.o
-
-#$(BUILDDIR)/sph_subs.o:
-#	$(CXX) $(CXXFLAGS) -c ../libnptm/sph_subs.cpp -o $(BUILDDIR)/sph_subs.o
-
-#$(BUILDDIR)/sphere.o:
-#	$(CXX) $(CXXFLAGS) -c sphere.cpp -o $(BUILDDIR)/sphere.o
+$(BUILDDIR)/np_sphere: $(CXX_SPH_OBJS)
+	$(CXX) $(CXXFLAGS) -o $(BUILDDIR)/np_sphere $(CXX_SPH_OBJS) $(CXXLDFLAGS) 
 
 clean:
-	rm -f $(BUILDDIR)/*.o
+	rm -f $(F_SPH_OBJS) $(CXX_SPH_OBJS)
 
 wipe:
-	rm -f $(BUILDDIR)/edfb_sph $(BUILDDIR)/sph $(BUILDDIR)/*.o
+	rm -f $(BUILDDIR)/edfb_sph $(BUILDDIR)/sph $(F_SPH_OBJS) $(CXX_SPH_OBJS)
 

src/trapping/Makefile

-BUILDDIR=../../build/trapping
+ifndef BUILDDIR
+override BUILDDIR=../../build/trapping
+endif
+ifndef OBJDIR
+override OBJDIR=../objects
+endif
 
 include ../make.inc
 
-#FC=gfortran
-#FCFLAGS=-std=legacy -O3
-#LFLAGS=
-#CXX=g++
-#CXXFLAGS=-O2 -ggdb -pg -coverage
-#CXXLFLAGS=-L/usr/lib64 -lhdf5_hl -lhdf5
+F_TRAP_OBJS=$(OBJDIR)/frfme.o $(OBJDIR)/lffft.o
 
-all: frfme lffft np_trapping
+CXX_TRAP_OBJS=$(OBJDIR)/np_trapping.o $(OBJDIR)/cfrfme.o $(OBJDIR)/clffft.o $(OBJDIR)/Parsers.o $(OBJDIR)/Commons.o $(OBJDIR)/Configuration.o $(OBJDIR)/file_io.o $(OBJDIR)/sph_subs.o $(OBJDIR)/tra_subs.o
 
-frfme: frfme.o
-	$(FC) $(FCFLAGS) -o $(BUILDDIR)/frfme $(BUILDDIR)/frfme.o $(LDFLAGS)
+all: $(BUILDDIR)/frfme $(BUILDDIR)/lffft $(BUILDDIR)/np_trapping
 
-lffft: lffft.o
-	$(FC) $(FCFLAGS) -o $(BUILDDIR)/lffft $(BUILDDIR)/lffft.o $(LDFLAGS)
+$(BUILDDIR)/frfme: $(OBJDIR)/frfme.o
+	$(FC) $(FCFLAGS) -o $(BUILDDIR)/frfme $(OBJDIR)/frfme.o $(LDFLAGS)
 
-np_trapping: $(BUILDDIR)/np_trapping.o $(BUILDDIR)/cfrfme.o $(BUILDDIR)/clffft.o $(BUILDDIR)/Parsers.o $(BUILDDIR)/Commons.o $(BUILDDIR)/Configuration.o $(BUILDDIR)/file_io.o $(BUILDDIR)/sph_subs.o $(BUILDDIR)/tra_subs.o
-	$(CXX) $(CXXFLAGS) -o $(BUILDDIR)/np_trapping $(BUILDDIR)/np_trapping.o $(BUILDDIR)/cfrfme.o $(BUILDDIR)/clffft.o $(BUILDDIR)/file_io.o $(BUILDDIR)/Parsers.o $(BUILDDIR)/Commons.o $(BUILDDIR)/Configuration.o $(BUILDDIR)/sph_subs.o $(BUILDDIR)/tra_subs.o $(CXXLDFLAGS) 
+$(BUILDDIR)/lffft: $(OBJDIR)/lffft.o
+	$(FC) $(FCFLAGS) -o $(BUILDDIR)/lffft $(OBJDIR)/lffft.o $(LDFLAGS)
 
-#$(BUILDDIR)/np_trapping.o:
-#	$(CXX) $(CXXFLAGS) np_trapping.cpp -c -o $(BUILDDIR)/np_trapping.o
-
-#$(BUILDDIR)/cfrfme.o:
-#	$(CXX) $(CXXFLAGS) frfme.cpp -c -o $(BUILDDIR)/cfrfme.o
-
-#$(BUILDDIR)/clffft.o:
-#	$(CXX) $(CXXFLAGS) lffft.cpp -c -o $(BUILDDIR)/clffft.o
-
-#$(BUILDDIR)/Commons.o:
-#	$(CXX) $(CXXFLAGS) ../libnptm/Commons.cpp -c -o $(BUILDDIR)/Commons.o
-
-#$(BUILDDIR)/Configuration.o:
-#	$(CXX) $(CXXFLAGS) ../libnptm/Configuration.cpp -c -o $(BUILDDIR)/Configuration.o
-
-#$(BUILDDIR)/file_io.o:
-#	$(CXX) $(CXXFLAGS) -c ../libnptm/file_io.cpp -o $(BUILDDIR)/file_io.o
-
-#$(BUILDDIR)/Parsers.o:
-#	$(CXX) $(CXXFLAGS) ../libnptm/Parsers.cpp -c -o $(BUILDDIR)/Parsers.o
-
-#$(BUILDDIR)/sph_subs.o:
-#	$(CXX) $(CXXFLAGS) ../libnptm/sph_subs.cpp -c -o $(BUILDDIR)/sph_subs.o
-
-#$(BUILDDIR)/tra_subs.o:
-#	$(CXX) $(CXXFLAGS) ../libnptm/tra_subs.cpp -c -o $(BUILDDIR)/tra_subs.o
+$(BUILDDIR)/np_trapping: $(CXX_TRAP_OBJS)
+	$(CXX) $(CXXFLAGS) -o $(BUILDDIR)/np_trapping $(CXX_TRAP_OBJS) $(CXXLDFLAGS) 
 
 clean:
-	rm -f $(BUILDDIR)/*.o
+	rm -f $(F_TRAP_OBJS) $(CXX_TRAP_OBJS)
 
 wipe:
-	rm -f $(BUILDDIR)/frfme $(BUILDDIR)/lffft $(BUILDDIR)/*.o
+	rm -f $(BUILDDIR)/frfme $(BUILDDIR)/lffft $(F_TRAP_OBJS) $(CXX_TRAP_OBJS)