MAINT: cleanup into src and include

Examples/Makefile.default

-HEATDTN_LIB_PATH=../dist/
-HEATDTN_INC_PATH=../
+HEATDTN_LIB_PATH=../dist
+HEATDTN_INC_PATH=../include
 
 #CXX=icpc
 #CXXFLAGS=-qopenmp -O3 -g -std=c++11 -w2 -I${HEATDTN_INC_PATH}
 #LDLIBSOPTIONS=-qopenmp -L${MKLROOT}/lib/intel64 -Wl,-rpath,'${MKLROOT}/lib/intel64' -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -L${HEATDTN_LIB_PATH} -Wl,-rpath,'${HEATDTN_LIB_PATH}' -lheatdtn
 
 CXX=g++
-CXXFLAGS=-fopenmp -O3 -g -std=c++11 -Wall -I${MKLROOT}/include -I${HEATDTN_INC_PATH}
+CXXFLAGS=-fopenmp -O3 -g -std=c++11 -Wall -I${HEATDTN_INC_PATH}
 LDLIBSOPTIONS=-fopenmp -L${MKLROOT}/lib/intel64 -Wl,-rpath,'${MKLROOT}/lib/intel64' -lmkl_intel_lp64 -lmkl_core -lmkl_gnu_thread -L${HEATDTN_LIB_PATH} -Wl,-rpath,'${HEATDTN_LIB_PATH}' -lheatdtn
 
 #########################DO NOT MODIFY BELOW THIS LINE##########################
@@ -16,15 +16,17 @@ COMPILELINE=${CXX} ${CXXFLAGS} -c
 
 OBJECTDIR=build
 
-CXXFILES=$(wildcard *.cpp)
+FILES=$(notdir $(wildcard src/*.cpp))
 
-OBJECTFILES=$(addprefix ${OBJECTDIR}/,$(CXXFILES:.cpp=.o))
+CXXFILES=$(addprefix src/,${FILES})
+
+OBJECTFILES=$(addprefix ${OBJECTDIR}/,$(FILES:.cpp=.o))
 
 build: ${OBJECTFILES}
 	mkdir -p dist
 	$(CXX) -o dist/testHeatDtN ${OBJECTFILES} ${LDLIBSOPTIONS}
 
-${OBJECTDIR}/%.o: %.cpp
+${OBJECTDIR}/%.o: src/%.cpp
 	mkdir -p ${OBJECTDIR}
 	rm -f "$@.d"
 	${COMPILELINE} -MMD -MP -MF "$@.d" -o $@ $<

Makefile.default

@@ -12,19 +12,21 @@ LDLIBSOPTIONS=-fopenmp -L${MKLROOT}/lib/intel64 -Wl,-rpath,'${MKLROOT}/lib/intel
 #########################DO NOT MODIFY BELOW THIS LINE##########################
 ################################################################################
 
-COMPILELINE=${CXX} ${CXXFLAGS} -c
+COMPILELINE=${CXX} ${CXXFLAGS} -I./include -I./src -c
 
 OBJECTDIR=build
 
-CXXFILES=$(wildcard *.cpp)
+FILES=$(notdir $(wildcard src/*.cpp))
 
-OBJECTFILES=$(addprefix ${OBJECTDIR}/,$(CXXFILES:.cpp=.o))
+CXXFILES=$(addprefix src/,${FILES})
+
+OBJECTFILES=$(addprefix ${OBJECTDIR}/,$(FILES:.cpp=.o))
 
 build: ${OBJECTFILES}
 	mkdir -p dist
 	$(CXX) -o dist/libheatdtn.so ${OBJECTFILES} ${LDLIBSOPTIONS} -shared -fPIC
 
-${OBJECTDIR}/%.o: %.cpp
+${OBJECTDIR}/%.o: src/%.cpp
 	mkdir -p ${OBJECTDIR}
 	rm -f "$@.d"
 	${COMPILELINE} -fPIC  -MMD -MP -MF "$@.d" -o $@ $<