Makefiles mods

lib/Makefile

-include ../config.mk
+include ../src/config.mk
 #
 OBJS = constants.o commLine.o geometry.o geometryDP.o stepPotentials.o intList.o txtUtils.o
 LIBFILE = libDiscrete.a

discrete/Makefile → src/Makefile

-include ../config.mk
+include config.mk
 #
 OBJS = IO.o random.o energy.o colisio.o DMD.o dims_utils.o least_sq_fit.o ANM.o
 MODS = paramSet.o  Structure.o doubleDMD.o ls_rmsd.o

Makefile → src/Makefile.orig

 V = 0.2.6
-EXEDIR =.
+EXEDIR =../bin
 #
 .PHONY: lib setup discrete
 #
 all: setup discrete
 	
 lib: 
-	cd lib; make
+	cd ../lib; make
 
 discrete: lib
-	cd discrete; make
+	make
 
 install: all
-	cp discrete/discrete $(EXEDIR)/discrete.exe
+	cp discrete $(EXEDIR)/discrete.exe
 
 clean:
 	cd lib;make clean
-	cd discrete; make clean
+	cd make clean
 	rm $(EXEDIR)/discrete.exe