diff --git a/Makefile b/Makefile
index 84636bd71..13ff05ed0 100644
--- a/Makefile
+++ b/Makefile
@@ -1,11 +1,16 @@
-export CC  = $(if $(shell which gcc-5 2>/dev/null),gcc-5,gcc)
-export CXX = $(if $(shell which g++-5 2>/dev/null),g++-5,g++)
+ifndef CC
+export CC  = $(if $(shell which gcc-5),gcc-5,gcc)
+endif
+ifndef CXX
+export CXX = $(if $(shell which g++-5),g++-5,g++)
+endif
 
-export MPICXX = mpicxx
 export LDFLAGS= -pthread -lm
-export CFLAGS = -Wall -O3 -msse2  -Wno-unknown-pragmas -funroll-loops
-# java include path
-export JAVAINCFLAGS = -I${JAVA_HOME}/include -I./java
+export CFLAGS= -Wall -O3 -msse2  -Wno-unknown-pragmas -funroll-loops -fPIC -Iinclude
+
+ifndef LINT_LANG
+	LINT_LANG= "all"
+endif
 
 ifeq ($(OS), Windows_NT)
 	export CXX = g++ -m64
@@ -16,199 +21,68 @@ UNAME= $(shell uname)
 
 ifeq ($(UNAME), Linux)
 	LDFLAGS += -lrt
-	JAVAINCFLAGS += -I${JAVA_HOME}/include/linux
-endif
-
-ifeq ($(UNAME), Darwin)
-	JAVAINCFLAGS += -I${JAVA_HOME}/include/darwin
 endif
 
 ifeq ($(no_omp),1)
 	CFLAGS += -DDISABLE_OPENMP
 else
-	#CFLAGS += -fopenmp
 	ifeq ($(omp_mac_static),1)
-		#CFLAGS += -fopenmp -Bstatic
 		CFLAGS += -static-libgcc -static-libstdc++ -L. -fopenmp
-		#LDFLAGS += -Wl,--whole-archive -lpthread -Wl --no-whole-archive
 	else
 		CFLAGS += -fopenmp
 	endif
 endif
 
 
-# by default use c++11
-ifeq ($(cxx11),1)
-	CFLAGS += -std=c++11
+ifndef DMLC_CORE
+	DMLC_CORE = dmlc-core
 endif
 
-# handling dmlc
-ifdef dmlc
-	ifndef config
-		ifneq ("$(wildcard $(dmlc)/config.mk)","")
-			config = $(dmlc)/config.mk
-		else
-			config = $(dmlc)/make/config.mk
-		endif
-	endif
-	include $(config)
-	include $(dmlc)/make/dmlc.mk
-	LDFLAGS+= $(DMLC_LDFLAGS)
-	LIBDMLC=$(dmlc)/libdmlc.a
-else
-	LIBDMLC=dmlc_simple.o
+ifndef RABIT
+	RABIT = rabit
 endif
 
-ifndef WITH_FPIC
-	WITH_FPIC = 1
-endif
-ifeq ($(WITH_FPIC), 1)
-	CFLAGS += -fPIC
-endif
-
-
-ifeq ($(OS), Windows_NT)
-	LIBRABIT = subtree/rabit/lib/librabit_empty.a
-	SLIB = wrapper/xgboost_wrapper.dll
-else
-	LIBRABIT = subtree/rabit/lib/librabit.a
-	SLIB = wrapper/libxgboostwrapper.so
-endif
-
-# java lib
-JLIB = java/libxgboost4j.so
-
 # specify tensor path
-BIN = xgboost
-MOCKBIN = xgboost.mock
-OBJ = updater.o gbm.o io.o main.o dmlc_simple.o
-MPIBIN =
-ifeq ($(WITH_FPIC), 1)
-	TARGET = $(BIN) $(OBJ) $(SLIB)
-else
-	TARGET = $(BIN)
-endif
+.PHONY: clean all lint
 
-ifndef LINT_LANG
-	LINT_LANG= "all"
-endif
+all: lib/libxgboost.a lib/libxgboost.so
 
-.PHONY: clean all mpi python Rpack lint
+$(DMLC_CORE)/libdmlc.a:
+	+ cd $(DMLC_CORE); make libdmlc.a; cd $(ROOTDIR)
 
-all: $(TARGET)
-mpi: $(MPIBIN)
+$(RABIT)/lib/librabit.a:
+	+ cd $(RABIT); make lib/librabit.a; cd $(ROOTDIR)
 
-python: wrapper/libxgboostwrapper.so
-# now the wrapper takes in two files. io and wrapper part
-updater.o: src/tree/updater.cpp  src/tree/*.hpp src/*.h src/tree/*.h src/utils/*.h
-dmlc_simple.o: src/io/dmlc_simple.cpp src/utils/*.h
-gbm.o: src/gbm/gbm.cpp src/gbm/*.hpp src/gbm/*.h
-io.o: src/io/io.cpp src/io/*.hpp src/utils/*.h src/learner/dmatrix.h src/*.h
-main.o: src/xgboost_main.cpp src/utils/*.h src/*.h src/learner/*.hpp src/learner/*.h
-xgboost:  updater.o gbm.o io.o main.o $(LIBRABIT) $(LIBDMLC)
-wrapper/xgboost_wrapper.dll wrapper/libxgboostwrapper.so: wrapper/xgboost_wrapper.cpp src/utils/*.h src/*.h src/learner/*.hpp src/learner/*.h  updater.o gbm.o io.o $(LIBRABIT) $(LIBDMLC)
+CFLAGS += -I$(DMLC_CORE)/include -I$(RABIT)/include
+Lib_DEP = $(DMLC_CORE)/libdmlc.a $(RABIT)/lib/librabit.a
 
-java: java/libxgboost4j.so
-java/libxgboost4j.so: java/xgboost4j_wrapper.cpp wrapper/xgboost_wrapper.cpp src/utils/*.h src/*.h src/learner/*.hpp src/learner/*.h  updater.o gbm.o io.o $(LIBRABIT) $(LIBDMLC)
+SRC = $(wildcard src/*.cc src/*/*.cc)
+OBJ = $(patsubst src/%.cc, build/%.o, $(SRC))
+LIB_DEP += $(DMLC_CORE)/libdmlc.a
+ALL_DEP = $(OBJ) $(LIB_DEP)
 
-# dependency on rabit
-subtree/rabit/lib/librabit.a: subtree/rabit/src/engine.cc
-	+	cd subtree/rabit;make lib/librabit.a; cd ../..
-subtree/rabit/lib/librabit_empty.a: subtree/rabit/src/engine_empty.cc
-	+	cd subtree/rabit;make lib/librabit_empty.a; cd ../..
-subtree/rabit/lib/librabit_mock.a: subtree/rabit/src/engine_mock.cc
-	+	cd subtree/rabit;make lib/librabit_mock.a; cd ../..
-subtree/rabit/lib/librabit_mpi.a: subtree/rabit/src/engine_mpi.cc
-	+	cd subtree/rabit;make lib/librabit_mpi.a; cd ../..
+build/%.o: src/%.cc
+	@mkdir -p $(@D)
+	$(CXX) -std=c++0x $(CFLAGS) -MM -MT build/$*.o $< >build/$*.d
+	$(CXX) -std=c++0x -c $(CFLAGS) -c $< -o $@
 
-$(BIN) :
-	$(CXX) $(CFLAGS) -fPIC -o $@ $(filter %.cpp %.o %.c %.cc %.a, $^) $(LDFLAGS)
+lib/libxgboost.a: $(ALL_DEP)
+	@mkdir -p $(@D)
+	ar crv $@ $(filter %.o, $?)
 
-$(MOCKBIN) :
-	$(CXX) $(CFLAGS) -o $@ $(filter %.cpp %.o %.c %.cc %.a, $^) $(LDFLAGS)
+lib/libxgboost.so: $(ALL_DEP)
+	@mkdir -p $(@D)
+	$(CXX) $(CFLAGS) -shared -o $@ $(filter %.o %.a, $^) $(LDFLAGS)
 
-$(SLIB) :
-	$(CXX) $(CFLAGS) -fPIC -shared -o $@ $(filter %.cpp %.o %.c %.a %.cc, $^) $(LDFLAGS) $(DLLFLAGS)
-
-$(JLIB) :
-	$(CXX) $(CFLAGS) -fPIC -shared -o $@ $(filter %.cpp %.o %.c %.a %.cc, $^) $(LDFLAGS)  $(JAVAINCFLAGS)
-
-$(OBJ) :
-	$(CXX) -c $(CFLAGS) -o $@ $(firstword $(filter %.cpp %.c %.cc, $^) )
-
-$(MPIOBJ) :
-	$(MPICXX) -c $(CFLAGS) -o $@ $(firstword $(filter %.cpp %.c, $^) )
-
-$(MPIBIN) :
-	$(MPICXX) $(CFLAGS) -o $@ $(filter %.cpp %.o %.c %.cc %.a, $^) $(LDFLAGS)
-
-install:
-	cp -f -r $(BIN)  $(INSTALL_PATH)
-
-Rpack:
-	make clean
-	cd subtree/rabit;make clean;cd ..
-	rm -rf xgboost xgboost*.tar.gz
-	cp -r R-package xgboost
-	rm -rf xgboost/src/*.o xgboost/src/*.so xgboost/src/*.dll
-	rm -rf xgboost/src/*/*.o
-	rm -rf subtree/rabit/src/*.o
-	rm -rf xgboost/demo/*.model xgboost/demo/*.buffer xgboost/demo/*.txt
-	rm -rf xgboost/demo/runall.R
-	cp -r src xgboost/src/src
-	mkdir xgboost/src/subtree
-	mkdir xgboost/src/subtree/rabit
-	cp -r subtree/rabit/include xgboost/src/subtree/rabit/include
-	cp -r subtree/rabit/src xgboost/src/subtree/rabit/src
-	rm -rf xgboost/src/subtree/rabit/src/*.o
-	mkdir xgboost/src/wrapper
-	cp  wrapper/xgboost_wrapper.h xgboost/src/wrapper
-	cp  wrapper/xgboost_wrapper.cpp xgboost/src/wrapper
-	cp ./LICENSE xgboost
-	cat R-package/src/Makevars|sed '2s/.*/PKGROOT=./' > xgboost/src/Makevars
-	cp xgboost/src/Makevars xgboost/src/Makevars.win
-	# R CMD build --no-build-vignettes xgboost
-	# R CMD build xgboost
-	# rm -rf xgboost
-	# R CMD check --as-cran xgboost*.tar.gz
-
-Rbuild:
-	make Rpack
-	R CMD build xgboost
-	rm -rf xgboost
-
-Rcheck:
-	make Rbuild
-	R CMD check --as-cran xgboost*.tar.gz
-
-pythonpack:
-	#for pip maintainer only
-	cd subtree/rabit;make clean;cd ..
-	rm -rf xgboost-deploy xgboost*.tar.gz
-	cp -r python-package xgboost-deploy
-	#cp *.md xgboost-deploy/
-	cp LICENSE xgboost-deploy/
-	cp Makefile xgboost-deploy/xgboost
-	cp -r wrapper xgboost-deploy/xgboost
-	cp -r subtree xgboost-deploy/xgboost
-	cp -r multi-node xgboost-deploy/xgboost
-	cp -r windows xgboost-deploy/xgboost
-	cp -r src xgboost-deploy/xgboost
-	cp python-package/setup_pip.py xgboost-deploy/setup.py
-	#make python
-
-pythonbuild:
-	make pythonpack
-	python setup.py install
-
-pythoncheck:
-	make pythonbuild
-	python -c 'import xgboost;print xgboost.core.find_lib_path()'
-
-# lint requires dmlc to be in current folder
 lint:
-	dmlc-core/scripts/lint.py xgboost $(LINT_LANG) src wrapper R-package python-package
+	python2 dmlc-core/scripts/lint.py xgboost ${LINT_LANG} include src
 
 clean:
-	$(RM) -rf $(OBJ) $(BIN) $(MPIBIN) $(MPIOBJ) $(SLIB) *.o  */*.o */*/*.o *~ */*~ */*/*~
-	cd subtree/rabit; make clean; cd ..
+	$(RM) -r build lib bin *~ */*~ */*/*~ */*/*/*~
+
+clean_all: clean
+	cd $(DMLC_CORE); make clean; cd -
+	cd $(PS_PATH); make clean; cd -
+
+-include build/*.d
+-include build/*/*.d