diff --git a/Makefile b/Makefile
index b19555fe962..75619c01da0 100644
--- a/Makefile
+++ b/Makefile
@@ -16,6 +16,10 @@ else
 	OTHER_BUILD_DIR := $(DEBUG_BUILD_DIR)
 endif
 
+# All of the directories containing code.
+SRC_DIRS := $(shell find * -type d -exec bash -c "find {} -maxdepth 1 \
+	\( -name '*.cpp' -o -name '*.proto' \) | grep -q ." \; -print)
+
 # The target shared library name
 LIB_BUILD_DIR := $(BUILD_DIR)/lib
 STATIC_NAME := $(LIB_BUILD_DIR)/lib$(PROJECT).a
@@ -26,8 +30,6 @@ DYNAMIC_NAME := $(LIB_BUILD_DIR)/lib$(PROJECT).so
 ##############################
 # CXX_SRCS are the source files excluding the test ones.
 CXX_SRCS := $(shell find src/$(PROJECT) ! -name "test_*.cpp" -name "*.cpp")
-# HXX_SRCS are the header files
-HXX_SRCS := $(shell find include/$(PROJECT) ! -name "test_*.hpp" -name "*.hpp")
 # CU_SRCS are the cuda source files
 CU_SRCS := $(shell find src/$(PROJECT) ! -name "test_*.cu" -name "*.cu")
 # TEST_SRCS are the test source files
@@ -36,8 +38,6 @@ TEST_SRCS := $(shell find src/$(PROJECT) -name "test_*.cpp")
 TEST_SRCS := $(filter-out $(TEST_MAIN_SRC), $(TEST_SRCS))
 TEST_CU_SRCS := $(shell find src/$(PROJECT) -name "test_*.cu")
 GTEST_SRC := src/gtest/gtest-all.cpp
-# TEST_HXX_SRCS are the test header files
-TEST_HXX_SRCS := $(shell find include/$(PROJECT) -name "test_*.hpp")
 # TOOL_SRCS are the source files for the tool binaries
 TOOL_SRCS := $(shell find tools -name "*.cpp")
 # EXAMPLE_SRCS are the source files for the example binaries
@@ -86,7 +86,6 @@ PROTO_GEN_HEADER_SRCS := $(addprefix $(PROTO_BUILD_DIR)/, \
 		$(notdir ${PROTO_SRCS:.proto=.pb.h}))
 PROTO_GEN_HEADER := $(addprefix $(PROTO_BUILD_INCLUDE_DIR)/, \
 		$(notdir ${PROTO_SRCS:.proto=.pb.h}))
-HXX_SRCS += $(PROTO_GEN_HEADER)
 PROTO_GEN_CC := $(addprefix $(BUILD_DIR)/, ${PROTO_SRCS:.proto=.pb.cc})
 PY_PROTO_BUILD_DIR := python/$(PROJECT)/proto
 PY_PROTO_INIT := python/$(PROJECT)/proto/__init__.py
@@ -96,25 +95,22 @@ PROTO_GEN_PY := $(foreach file,${PROTO_SRCS:.proto=_pb2.py}, \
 # These objects will be linked into the final shared library, so we
 # exclude the tool, example, and test objects.
 CXX_OBJS := $(addprefix $(BUILD_DIR)/, ${CXX_SRCS:.cpp=.o})
-CU_OBJS := $(addprefix $(BUILD_DIR)/, ${CU_SRCS:.cu=.cuo})
+CU_OBJS := $(addprefix $(BUILD_DIR)/cuda/, ${CU_SRCS:.cu=.o})
 PROTO_OBJS := ${PROTO_GEN_CC:.cc=.o}
-OBJ_BUILD_DIR := $(BUILD_DIR)/src/$(PROJECT)
-LAYER_BUILD_DIR := $(OBJ_BUILD_DIR)/layers
-UTIL_BUILD_DIR := $(OBJ_BUILD_DIR)/util
 OBJS := $(PROTO_OBJS) $(CXX_OBJS) $(CU_OBJS)
 # tool, example, and test objects
 TOOL_OBJS := $(addprefix $(BUILD_DIR)/, ${TOOL_SRCS:.cpp=.o})
 TOOL_BUILD_DIR := $(BUILD_DIR)/tools
-TEST_BUILD_DIR := $(BUILD_DIR)/src/$(PROJECT)/test
+TEST_CXX_BUILD_DIR := $(BUILD_DIR)/src/$(PROJECT)/test
+TEST_CU_BUILD_DIR := $(BUILD_DIR)/cuda/src/$(PROJECT)/test
 TEST_CXX_OBJS := $(addprefix $(BUILD_DIR)/, ${TEST_SRCS:.cpp=.o})
-TEST_CU_OBJS := $(addprefix $(BUILD_DIR)/, ${TEST_CU_SRCS:.cu=.cuo})
+TEST_CU_OBJS := $(addprefix $(BUILD_DIR)/cuda/, ${TEST_CU_SRCS:.cu=.o})
 TEST_OBJS := $(TEST_CXX_OBJS) $(TEST_CU_OBJS)
 GTEST_OBJ := $(addprefix $(BUILD_DIR)/, ${GTEST_SRC:.cpp=.o})
-GTEST_BUILD_DIR := $(dir $(GTEST_OBJ))
 EXAMPLE_OBJS := $(addprefix $(BUILD_DIR)/, ${EXAMPLE_SRCS:.cpp=.o})
-EXAMPLE_BUILD_DIR := $(BUILD_DIR)/examples
-EXAMPLE_BUILD_DIRS := $(EXAMPLE_BUILD_DIR)
-EXAMPLE_BUILD_DIRS += $(foreach obj,$(EXAMPLE_OBJS),$(dir $(obj)))
+# Output files for automatic dependency generation
+DEPS := ${CXX_OBJS:.o=.d} ${CU_OBJS:.o=.d} ${TEST_CXX_OBJS:.o=.d} \
+	${TEST_CU_OBJS:.o=.d}
 # tool, example, and test bins
 TOOL_BINS := ${TOOL_OBJS:.o=.bin}
 EXAMPLE_BINS := ${EXAMPLE_OBJS:.o=.bin}
@@ -137,11 +133,11 @@ TEST_ALL_DYNLINK_BIN := $(TEST_BIN_DIR)/test_all_dynamic_link.testbin
 ##############################
 WARNS_EXT := warnings.txt
 CXX_WARNS := $(addprefix $(BUILD_DIR)/, ${CXX_SRCS:.cpp=.o.$(WARNS_EXT)})
-CU_WARNS := $(addprefix $(BUILD_DIR)/, ${CU_SRCS:.cu=.cuo.$(WARNS_EXT)})
+CU_WARNS := $(addprefix $(BUILD_DIR)/cuda/, ${CU_SRCS:.cu=.o.$(WARNS_EXT)})
 TOOL_WARNS := $(addprefix $(BUILD_DIR)/, ${TOOL_SRCS:.cpp=.o.$(WARNS_EXT)})
 EXAMPLE_WARNS := $(addprefix $(BUILD_DIR)/, ${EXAMPLE_SRCS:.cpp=.o.$(WARNS_EXT)})
 TEST_WARNS := $(addprefix $(BUILD_DIR)/, ${TEST_SRCS:.cpp=.o.$(WARNS_EXT)})
-TEST_CU_WARNS := $(addprefix $(BUILD_DIR)/, ${TEST_CU_SRCS:.cu=.cuo.$(WARNS_EXT)})
+TEST_CU_WARNS := $(addprefix $(BUILD_DIR)/cuda/, ${TEST_CU_SRCS:.cu=.o.$(WARNS_EXT)})
 ALL_CXX_WARNS := $(CXX_WARNS) $(TOOL_WARNS) $(EXAMPLE_WARNS) $(TEST_WARNS)
 ALL_CU_WARNS := $(CU_WARNS) $(TEST_CU_WARNS)
 ALL_WARNS := $(ALL_CXX_WARNS) $(ALL_CU_WARNS)
@@ -183,14 +179,10 @@ ifneq ($(strip $(DISTRIBUTE_DIR)),distribute)
 		DIST_ALIASES += distribute
 endif
 
-ALL_BUILD_DIRS := $(sort \
-		$(BUILD_DIR) $(LIB_BUILD_DIR) $(OBJ_BUILD_DIR) \
-		$(LAYER_BUILD_DIR) $(UTIL_BUILD_DIR) $(TOOL_BUILD_DIR) \
-		$(TEST_BUILD_DIR) $(TEST_BIN_DIR) $(GTEST_BUILD_DIR) \
-		$(EXAMPLE_BUILD_DIRS) \
-		$(LINT_OUTPUT_DIR) \
-		$(PROTO_BUILD_DIR) $(PROTO_BUILD_INCLUDE_DIR) $(PY_PROTO_BUILD_DIR) \
-		$(DISTRIBUTE_SUBDIRS))
+ALL_BUILD_DIRS := $(sort $(BUILD_DIR) $(addprefix $(BUILD_DIR)/, $(SRC_DIRS)) \
+	$(addprefix $(BUILD_DIR)/cuda/, $(SRC_DIRS)) \
+	$(LIB_BUILD_DIR) $(TEST_BIN_DIR) $(PY_PROTO_BUILD_DIR) $(LINT_OUTPUT_DIR) \
+	$(DISTRIBUTE_SUBDIRS) $(PROTO_BUILD_INCLUDE_DIR))
 
 ##############################
 # Set directory for Doxygen-generated documentation
@@ -322,6 +314,9 @@ LIBRARY_DIRS += $(BLAS_LIB)
 
 LIBRARY_DIRS += $(LIB_BUILD_DIR)
 
+# Automatic dependency generation (nvcc is handled separately)
+CXXFLAGS += -MMD -MP
+
 # Complete build flags.
 COMMON_FLAGS += $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir))
 CXXFLAGS += -pthread -fPIC $(COMMON_FLAGS) $(WARNINGS)
@@ -445,9 +440,7 @@ $(EMPTY_WARN_REPORT): $(ALL_WARNS) | $(BUILD_DIR)
 	  $(RM) $(NONEMPTY_WARN_REPORT); \
 	  echo "No compiler warnings!";
 
-$(ALL_CXX_WARNS): %.o.$(WARNS_EXT) : %.o
-
-$(ALL_CU_WARNS): %.cuo.$(WARNS_EXT) : %.cuo
+$(ALL_WARNS): %.o.$(WARNS_EXT) : %.o
 
 $(BUILD_DIR_LINK): $(BUILD_DIR)/.linked
 
@@ -472,15 +465,22 @@ $(STATIC_NAME): $(OBJS) | $(LIB_BUILD_DIR)
 	ar rcs $@ $(OBJS)
 	@ echo
 
-$(TEST_BUILD_DIR)/%.o: src/$(PROJECT)/test/%.cpp $(HXX_SRCS) $(TEST_HXX_SRCS) \
-		| $(TEST_BUILD_DIR)
+$(BUILD_DIR)/%.o: %.cpp | $(ALL_BUILD_DIRS)
+	$(CXX) $< $(CXXFLAGS) -c -o $@ 2> $@.$(WARNS_EXT) \
+		|| (cat $@.$(WARNS_EXT); exit 1)
+	@ cat $@.$(WARNS_EXT)
+	@ echo
+
+$(PROTO_BUILD_DIR)/%.pb.o: $(PROTO_BUILD_DIR)/%.pb.cc $(PROTO_GEN_HEADER) \
+		| $(PROTO_BUILD_DIR)
 	$(CXX) $< $(CXXFLAGS) -c -o $@ 2> $@.$(WARNS_EXT) \
 		|| (cat $@.$(WARNS_EXT); exit 1)
 	@ cat $@.$(WARNS_EXT)
 	@ echo
 
-$(TEST_BUILD_DIR)/%.cuo: src/$(PROJECT)/test/%.cu $(HXX_SRCS) $(TEST_HXX_SRCS) \
-		| $(TEST_BUILD_DIR)
+$(BUILD_DIR)/cuda/%.o: %.cu | $(ALL_BUILD_DIRS)
+	$(CUDA_DIR)/bin/nvcc $(NVCCFLAGS) $(CUDA_ARCH) -M $< -o ${@:.o=.d} \
+		-odir $(@D)
 	$(CUDA_DIR)/bin/nvcc $(NVCCFLAGS) $(CUDA_ARCH) -c $< -o $@ 2> $@.$(WARNS_EXT) \
 		|| (cat $@.$(WARNS_EXT); exit 1)
 	@ cat $@.$(WARNS_EXT)
@@ -498,14 +498,14 @@ $(TEST_ALL_DYNLINK_BIN): $(TEST_MAIN_SRC) $(TEST_OBJS) $(GTEST_OBJ) $(DYNAMIC_NA
 		-o $@ $(LINKFLAGS) $(LDFLAGS) -l$(PROJECT) -Wl,-rpath,$(LIB_BUILD_DIR)
 	@ echo
 
-$(TEST_CU_BINS): $(TEST_BIN_DIR)/%.testbin: $(TEST_BUILD_DIR)/%.cuo $(GTEST_OBJ) $(STATIC_NAME) \
-		| $(TEST_BIN_DIR)
+$(TEST_CU_BINS): $(TEST_BIN_DIR)/%.testbin: $(TEST_CU_BUILD_DIR)/%.o \
+	$(GTEST_OBJ) $(STATIC_NAME) | $(TEST_BIN_DIR)
 	$(CXX) $(TEST_MAIN_SRC) $< $(GTEST_OBJ) $(STATIC_LINK_COMMAND) \
 		-o $@ $(LINKFLAGS) $(LDFLAGS)
 	@ echo
 
-$(TEST_CXX_BINS): $(TEST_BIN_DIR)/%.testbin: $(TEST_BUILD_DIR)/%.o $(GTEST_OBJ) $(STATIC_NAME) \
-		| $(TEST_BIN_DIR)
+$(TEST_CXX_BINS): $(TEST_BIN_DIR)/%.testbin: $(TEST_CXX_BUILD_DIR)/%.o \
+	$(GTEST_OBJ) $(STATIC_NAME) | $(TEST_BIN_DIR)
 	$(CXX) $(TEST_MAIN_SRC) $< $(GTEST_OBJ) $(STATIC_LINK_COMMAND) \
 		-o $@ $(LINKFLAGS) $(LDFLAGS)
 	@ echo
@@ -515,72 +515,10 @@ $(TOOL_BUILD_DIR)/%: $(TOOL_BUILD_DIR)/%.bin | $(TOOL_BUILD_DIR)
 	@ $(RM) $@
 	@ ln -s $(abspath $<) $@
 
-$(TOOL_BINS): %.bin : %.o $(STATIC_NAME)
+$(TOOL_BINS) $(EXAMPLE_BINS): %.bin : %.o $(STATIC_NAME)
 	$(CXX) $< $(STATIC_LINK_COMMAND) -o $@ $(LINKFLAGS) $(LDFLAGS)
 	@ echo
 
-$(EXAMPLE_BINS): %.bin : %.o $(STATIC_NAME)
-	$(CXX) $< $(STATIC_LINK_COMMAND) -o $@ $(LINKFLAGS) $(LDFLAGS)
-	@ echo
-
-$(LAYER_BUILD_DIR)/%.o: src/$(PROJECT)/layers/%.cpp $(HXX_SRCS) \
-		| $(LAYER_BUILD_DIR)
-	$(CXX) $< $(CXXFLAGS) -c -o $@ 2> $@.$(WARNS_EXT) \
-		|| (cat $@.$(WARNS_EXT); exit 1)
-	@ cat $@.$(WARNS_EXT)
-	@ echo
-
-$(PROTO_BUILD_DIR)/%.pb.o: $(PROTO_BUILD_DIR)/%.pb.cc $(PROTO_GEN_HEADER) \
-		| $(PROTO_BUILD_DIR)
-	$(CXX) $< $(CXXFLAGS) -c -o $@ 2> $@.$(WARNS_EXT) \
-		|| (cat $@.$(WARNS_EXT); exit 1)
-	@ cat $@.$(WARNS_EXT)
-	@ echo
-
-$(UTIL_BUILD_DIR)/%.o: src/$(PROJECT)/util/%.cpp $(HXX_SRCS) | $(UTIL_BUILD_DIR)
-	$(CXX) $< $(CXXFLAGS) -c -o $@ 2> $@.$(WARNS_EXT) \
-		|| (cat $@.$(WARNS_EXT); exit 1)
-	@ cat $@.$(WARNS_EXT)
-	@ echo
-
-$(GTEST_OBJ): $(GTEST_SRC) | $(GTEST_BUILD_DIR)
-	$(CXX) $< $(CXXFLAGS) -c -o $@ 2> $@.$(WARNS_EXT) \
-		|| (cat $@.$(WARNS_EXT); exit 1)
-	@ cat $@.$(WARNS_EXT)
-	@ echo
-
-$(LAYER_BUILD_DIR)/%.cuo: src/$(PROJECT)/layers/%.cu $(HXX_SRCS) \
-		| $(LAYER_BUILD_DIR)
-	$(CUDA_DIR)/bin/nvcc $(NVCCFLAGS) $(CUDA_ARCH) -c $< -o $@ 2> $@.$(WARNS_EXT) \
-		|| (cat $@.$(WARNS_EXT); exit 1)
-	@ cat $@.$(WARNS_EXT)
-	@ echo
-
-$(UTIL_BUILD_DIR)/%.cuo: src/$(PROJECT)/util/%.cu | $(UTIL_BUILD_DIR)
-	$(CUDA_DIR)/bin/nvcc $(NVCCFLAGS) $(CUDA_ARCH) -c $< -o $@ 2> $@.$(WARNS_EXT) \
-		|| (cat $@.$(WARNS_EXT); exit 1)
-	@ cat $@.$(WARNS_EXT)
-	@ echo
-
-$(TOOL_BUILD_DIR)/%.o: tools/%.cpp $(PROTO_GEN_HEADER) | $(TOOL_BUILD_DIR)
-	$(CXX) $< $(CXXFLAGS) -c -o $@ 2> $@.$(WARNS_EXT) \
-		|| (cat $@.$(WARNS_EXT); exit 1)
-	@ cat $@.$(WARNS_EXT)
-	@ echo
-
-$(EXAMPLE_BUILD_DIR)/%.o: examples/%.cpp $(PROTO_GEN_HEADER) \
-		| $(EXAMPLE_BUILD_DIRS)
-	$(CXX) $< $(CXXFLAGS) -c -o $@ 2> $@.$(WARNS_EXT) \
-		|| (cat $@.$(WARNS_EXT); exit 1)
-	@ cat $@.$(WARNS_EXT)
-	@ echo
-
-$(BUILD_DIR)/src/$(PROJECT)/%.o: src/$(PROJECT)/%.cpp $(HXX_SRCS)
-	$(CXX) $< $(CXXFLAGS) -c -o $@ 2> $@.$(WARNS_EXT) \
-		|| (cat $@.$(WARNS_EXT); exit 1)
-	@ cat $@.$(WARNS_EXT)
-	@ echo
-
 proto: $(PROTO_GEN_CC) $(PROTO_GEN_HEADER)
 
 $(PROTO_BUILD_DIR)/%.pb.cc $(PROTO_BUILD_DIR)/%.pb.h : \
@@ -629,7 +567,7 @@ superclean: clean supercleanfiles
 
 $(DIST_ALIASES): $(DISTRIBUTE_DIR)
 
-$(DISTRIBUTE_DIR): all py $(HXX_SRCS) | $(DISTRIBUTE_SUBDIRS)
+$(DISTRIBUTE_DIR): all py | $(DISTRIBUTE_SUBDIRS)
 	# add include
 	cp -r include $(DISTRIBUTE_DIR)/
 	mkdir -p $(DISTRIBUTE_DIR)/include/caffe/proto
@@ -642,3 +580,5 @@ $(DISTRIBUTE_DIR): all py $(HXX_SRCS) | $(DISTRIBUTE_SUBDIRS)
 	cp $(DYNAMIC_NAME) $(DISTRIBUTE_DIR)/lib
 	# add python - it's not the standard way, indeed...
 	cp -r python $(DISTRIBUTE_DIR)/python
+
+-include $(DEPS)