diff --git a/.gitignore b/.gitignore
index 3997e463cdb..5aeb3dc24e2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -34,6 +34,7 @@ build/*
 distribute/*
 *.testbin
 *.bin
+python/caffe/proto/
 
 # Editor temporaries
 *.swp
diff --git a/Makefile b/Makefile
index acef07d6837..83117e3ae41 100644
--- a/Makefile
+++ b/Makefile
@@ -1,16 +1,13 @@
-# The makefile for caffe. Extremely hacky.
+# The makefile for caffe. Pretty hacky.
 PROJECT := caffe
-TEST_GPUID := 0
 
-include Makefile.config
-
-##############################################################################
-# After this line, things should happen automatically.
-##############################################################################
+CONFIG_FILE := Makefile.config
+include $(CONFIG_FILE)
 
 # The target static library and shared library name
-NAME := lib$(PROJECT).so
-STATIC_NAME := lib$(PROJECT).a
+LIB_BUILD_DIR := $(BUILD_DIR)/lib
+NAME := $(LIB_BUILD_DIR)/lib$(PROJECT).so
+STATIC_NAME := $(LIB_BUILD_DIR)/lib$(PROJECT).a
 
 ##############################
 # Get all source files
@@ -32,8 +29,15 @@ TEST_HDRS := $(shell find src/$(PROJECT) -name "test_*.hpp")
 TOOL_SRCS := $(shell find tools -name "*.cpp")
 # EXAMPLE_SRCS are the source files for the example binaries
 EXAMPLE_SRCS := $(shell find examples -name "*.cpp")
+# BUILD_INCLUDE_DIR contains any generated header files we want to include.
+BUILD_INCLUDE_DIR := $(BUILD_DIR)/src
 # PROTO_SRCS are the protocol buffer definitions
-PROTO_SRCS := $(wildcard src/$(PROJECT)/proto/*.proto)
+PROTO_SRC_DIR := src/$(PROJECT)/proto
+PROTO_SRCS := $(wildcard $(PROTO_SRC_DIR)/*.proto)
+# PROTO_BUILD_DIR will contain the .cc and obj files generated from
+# PROTO_SRCS; PROTO_BUILD_INCLUDE_DIR will contain the .h header files
+PROTO_BUILD_DIR := $(BUILD_DIR)/$(PROTO_SRC_DIR)
+PROTO_BUILD_INCLUDE_DIR := $(BUILD_INCLUDE_DIR)/$(PROJECT)/proto
 # NONGEN_CXX_SRCS includes all source/header files except those generated
 # automatically (e.g., by proto).
 NONGEN_CXX_SRCS := $(shell find \
@@ -51,32 +55,54 @@ PY$(PROJECT)_SRC := python/$(PROJECT)/_$(PROJECT).cpp
 PY$(PROJECT)_SO := python/$(PROJECT)/_$(PROJECT).so
 # MAT$(PROJECT)_SRC is the matlab wrapper for $(PROJECT)
 MAT$(PROJECT)_SRC := matlab/$(PROJECT)/mat$(PROJECT).cpp
-MAT$(PROJECT)_SO := matlab/$(PROJECT)/$(PROJECT)
+ifneq ($(MATLAB_DIR),)
+	MAT_SO_EXT := $(shell $(MATLAB_DIR)/bin/mexext)
+endif
+MAT$(PROJECT)_SO := matlab/$(PROJECT)/$(PROJECT).$(MAT_SO_EXT)
 
 ##############################
 # Derive generated files
 ##############################
 # The generated files for protocol buffers
-PROTO_GEN_HEADER := ${PROTO_SRCS:.proto=.pb.h}
-PROTO_GEN_CC := ${PROTO_SRCS:.proto=.pb.cc}
-PROTO_GEN_PY := ${PROTO_SRCS:.proto=_pb2.py}
+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
+PROTO_GEN_PY := $(foreach file,${PROTO_SRCS:.proto=_pb2.py}, \
+		$(PY_PROTO_BUILD_DIR)/$(notdir $(file)))
 # The objects corresponding to the source files
 # 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})
-PROTO_OBJS := $(addprefix $(BUILD_DIR)/, ${PROTO_GEN_CC:.cc=.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})
-EXAMPLE_OBJS := $(addprefix $(BUILD_DIR)/, ${EXAMPLE_SRCS:.cpp=.o})
+TOOL_BUILD_DIR := $(BUILD_DIR)/tools
+TEST_BUILD_DIR := $(BUILD_DIR)/src/$(PROJECT)/test
 TEST_OBJS := $(addprefix $(BUILD_DIR)/, ${TEST_SRCS:.cpp=.o})
 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)))
 # tool, example, and test bins
 TOOL_BINS := ${TOOL_OBJS:.o=.bin}
 EXAMPLE_BINS := ${EXAMPLE_OBJS:.o=.bin}
-TEST_BINS := ${TEST_OBJS:.o=.testbin}
-TEST_ALL_BIN := $(BUILD_DIR)/src/$(PROJECT)/test/test_all.testbin
+# Put the test binaries in build/test for convenience.
+TEST_BIN_DIR := $(BUILD_DIR)/test
+TEST_BINS := $(addsuffix .testbin,$(addprefix $(TEST_BIN_DIR)/, \
+		$(foreach obj,$(TEST_OBJS),$(basename $(notdir $(obj))))))
+TEST_ALL_BIN := $(TEST_BIN_DIR)/test_all.testbin
 
 ##############################
 # Derive include and lib directories
@@ -86,6 +112,7 @@ CUDA_LIB_DIR := $(CUDA_DIR)/lib64 $(CUDA_DIR)/lib
 MKL_INCLUDE_DIR := $(MKL_DIR)/include
 MKL_LIB_DIR := $(MKL_DIR)/lib $(MKL_DIR)/lib/intel64
 
+INCLUDE_DIRS += $(BUILD_INCLUDE_DIR)
 INCLUDE_DIRS += ./src ./include $(CUDA_INCLUDE_DIR)
 LIBRARY_DIRS += $(CUDA_LIB_DIR)
 LIBRARIES := cudart cublas curand \
@@ -97,7 +124,26 @@ LIBRARIES := cudart cublas curand \
 PYTHON_LIBRARIES := boost_python python2.7
 WARNINGS := -Wall
 
-ifdef DEBUG
+##############################
+# Set build directories
+##############################
+
+DISTRIBUTE_SUBDIRS := $(DISTRIBUTE_DIR)/bin $(DISTRIBUTE_DIR)/lib
+DIST_ALIASES := dist
+ifneq ($(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) \
+		$(PROTO_BUILD_DIR) $(PROTO_BUILD_INCLUDE_DIR) $(PY_PROTO_BUILD_DIR) \
+		$(DISTRIBUTE_SUBDIRS))
+
+DEBUG ?= 0
+ifeq ($(DEBUG), 1)
 	COMMON_FLAGS := -DDEBUG -g -O0
 else
 	COMMON_FLAGS := -DNDEBUG -O2
@@ -121,156 +167,201 @@ LDFLAGS += $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) \
 		$(foreach library,$(LIBRARIES),-l$(library))
 PYTHON_LDFLAGS := $(LDFLAGS) $(foreach library,$(PYTHON_LIBRARIES),-l$(library))
 
+# 'superclean' target recursively* deletes all files ending with an extension
+# in $(SUPERCLEAN_EXTS) below.  This may be useful if you've built older
+# versions of Caffe that do not place all generated files in a location known
+# to the 'clean' target.
+#
+# 'supercleanlist' will list the files to be deleted by make superclean.
+#
+# * Recursive with the exception that symbolic links are never followed, per the
+# default behavior of 'find'.
+SUPERCLEAN_EXTS := .so .a .o .bin .testbin .pb.cc .pb.h _pb2.py .cuo
+
 ##############################
 # Define build targets
 ##############################
-.PHONY: all init test clean linecount lint tools examples py mat distribute \
-        py$(PROJECT) mat$(PROJECT) proto runtest
-
-all: init $(NAME) $(STATIC_NAME) tools examples
-	@echo $(CXX_OBJS)
+.PHONY: all test clean linecount lint tools examples $(DIST_ALIASES) \
+	py mat py$(PROJECT) mat$(PROJECT) proto runtest \
+	superclean supercleanlist supercleanfiles
 
-init:
-	@ mkdir -p $(foreach obj,$(OBJS),$(dir $(obj)))
-	@ mkdir -p $(foreach obj,$(TOOL_OBJS),$(dir $(obj)))
-	@ mkdir -p $(foreach obj,$(EXAMPLE_OBJS),$(dir $(obj)))
-	@ mkdir -p $(foreach obj,$(TEST_OBJS),$(dir $(obj)))
-	@ mkdir -p $(foreach obj,$(GTEST_OBJ),$(dir $(obj)))
+all: $(NAME) $(STATIC_NAME) tools examples
 
 linecount: clean
 	cloc --read-lang-def=$(PROJECT).cloc src/$(PROJECT)/
 
 lint: $(LINT_REPORT)
 
-$(LINT_REPORT): $(NONGEN_CXX_SRCS)
-	@ mkdir -p $(BUILD_DIR)
+$(LINT_REPORT): $(NONGEN_CXX_SRCS) | $(BUILD_DIR)
 	@ (python ./scripts/cpp_lint.py $(NONGEN_CXX_SRCS) > $(LINT_REPORT) 2>&1 \
-		&& (rm -f $(FAILED_LINT_REPORT); echo "No lint errors!")) || ( \
+		&& ($(RM) $(FAILED_LINT_REPORT); echo "No lint errors!")) || ( \
 			mv $(LINT_REPORT) $(FAILED_LINT_REPORT); \
 			grep -v "^Done processing " $(FAILED_LINT_REPORT); \
 			echo "Found 1 or more lint errors; see log at $(FAILED_LINT_REPORT)"; \
 			exit 1)
 
-test: init $(TEST_BINS) $(TEST_ALL_BIN)
+test: $(TEST_ALL_BIN) $(TEST_BINS)
 
-tools: init $(TOOL_BINS)
+tools: $(TOOL_BINS)
 
-examples: init $(EXAMPLE_BINS)
+examples: $(EXAMPLE_BINS)
 
 py$(PROJECT): py
 
-py: init $(STATIC_NAME) $(PY$(PROJECT)_SRC) $(PROTO_GEN_PY)
-	$(CXX) -shared -o $(PY$(PROJECT)_SO) $(PY$(PROJECT)_SRC) \
+py: $(PY$(PROJECT)_SO) $(PROTO_GEN_PY)
+
+$(PY$(PROJECT)_SO): $(STATIC_NAME) $(PY$(PROJECT)_SRC)
+	$(CXX) -shared -o $@ $(PY$(PROJECT)_SRC) \
 		$(STATIC_NAME) $(CXXFLAGS) $(PYTHON_LDFLAGS)
-	@echo
+	@ echo
 
 mat$(PROJECT): mat
 
-mat: init $(STATIC_NAME) $(MAT$(PROJECT)_SRC)
-	$(MATLAB_DIR)/bin/mex $(MAT$(PROJECT)_SRC) $(STATIC_NAME) \
-		CXXFLAGS="\$$CXXFLAGS $(CXXFLAGS) $(WARNINGS)" \
-		CXXLIBS="\$$CXXLIBS $(LDFLAGS)" \
-		-o $(MAT$(PROJECT)_SO)
-	@echo
-
-$(NAME): init $(PROTO_OBJS) $(OBJS)
-	$(CXX) -shared -o $(NAME) $(OBJS) $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
-	@echo
+mat: $(MAT$(PROJECT)_SO)
 
-$(STATIC_NAME): init $(PROTO_OBJS) $(OBJS)
-	ar rcs $(STATIC_NAME) $(PROTO_OBJS) $(OBJS)
-	@echo
+$(MAT$(PROJECT)_SO): $(MAT$(PROJECT)_SRC) $(STATIC_NAME)
+	@ if [ -z "$(MATLAB_DIR)" ]; then \
+		echo "MATLAB_DIR must be specified in $(CONFIG_FILE)" \
+			"to build mat$(PROJECT)."; \
+		exit 1; \
+	fi
+	$(MATLAB_DIR)/bin/mex $(MAT$(PROJECT)_SRC) $(STATIC_NAME) \
+			CXXFLAGS="\$$CXXFLAGS $(CXXFLAGS) $(WARNINGS)" \
+			CXXLIBS="\$$CXXLIBS $(LDFLAGS)" -o $@
+	@ echo
 
 runtest: $(TEST_ALL_BIN)
 	$(TEST_ALL_BIN) $(TEST_GPUID)
 
-$(TEST_BINS): %.testbin : %.o $(GTEST_OBJ) $(STATIC_NAME) $(TEST_HDRS)
-	$(CXX) $(TEST_MAIN_SRC) $< $(GTEST_OBJ) $(STATIC_NAME) -o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
+$(ALL_BUILD_DIRS):
+	@ mkdir -p $@
+
+$(NAME): $(PROTO_OBJS) $(OBJS) | $(LIB_BUILD_DIR)
+	$(CXX) -shared -o $@ $(OBJS) $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
+	@ echo
+
+$(STATIC_NAME): $(PROTO_OBJS) $(OBJS) | $(LIB_BUILD_DIR)
+	ar rcs $@ $(PROTO_OBJS) $(OBJS)
+	@ echo
+
+$(TEST_BUILD_DIR)/%.o: src/$(PROJECT)/test/%.cpp $(HXX_SRCS) $(TEST_HDRS) \
+		| $(TEST_BUILD_DIR)
+	$(CXX) $< $(CXXFLAGS) -c -o $@
+	@ echo
+
+$(TEST_ALL_BIN): $(TEST_MAIN_SRC) $(TEST_OBJS) $(GTEST_OBJ) $(STATIC_NAME) \
+		| $(TEST_BIN_DIR)
+	$(CXX) $(TEST_MAIN_SRC) $(TEST_OBJS) $(GTEST_OBJ) $(STATIC_NAME) \
+		-o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
+	@ echo
 
-$(TEST_ALL_BIN): $(GTEST_OBJ) $(STATIC_NAME) $(TEST_OBJS)
-	$(CXX) $(TEST_MAIN_SRC) $(TEST_OBJS) $(GTEST_OBJ) $(STATIC_NAME) -o $(TEST_ALL_BIN) $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
+$(TEST_BIN_DIR)/%.testbin: $(TEST_BUILD_DIR)/%.o $(GTEST_OBJ) $(STATIC_NAME) \
+		| $(TEST_BIN_DIR)
+	$(CXX) $(TEST_MAIN_SRC) $< $(GTEST_OBJ) $(STATIC_NAME) \
+		-o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
+	@ echo
 
 $(TOOL_BINS): %.bin : %.o $(STATIC_NAME)
 	$(CXX) $< $(STATIC_NAME) -o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
-	@echo
+	@ echo
 
 $(EXAMPLE_BINS): %.bin : %.o $(STATIC_NAME)
 	$(CXX) $< $(STATIC_NAME) -o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
-	@echo
+	@ echo
 
-$(OBJS): $(PROTO_GEN_CC) $(HXX_SRCS)
-
-$(BUILD_DIR)/src/$(PROJECT)/%.o: src/$(PROJECT)/%.cpp
+$(LAYER_BUILD_DIR)/%.o: src/$(PROJECT)/layers/%.cpp $(HXX_SRCS) \
+		| $(LAYER_BUILD_DIR)
 	$(CXX) $< $(CXXFLAGS) -c -o $@
-	@echo
+	@ echo
 
-$(BUILD_DIR)/src/$(PROJECT)/layers/%.o: src/$(PROJECT)/layers/%.cpp
+$(PROTO_BUILD_DIR)/%.pb.o: $(PROTO_BUILD_DIR)/%.pb.cc $(PROTO_GEN_HEADER) \
+		| $(PROTO_BUILD_DIR)
 	$(CXX) $< $(CXXFLAGS) -c -o $@
-	@echo
+	@ echo
 
-$(BUILD_DIR)/src/$(PROJECT)/proto/%.o: src/$(PROJECT)/proto/%.cc
+$(UTIL_BUILD_DIR)/%.o: src/$(PROJECT)/util/%.cpp $(HXX_SRCS) | $(UTIL_BUILD_DIR)
 	$(CXX) $< $(CXXFLAGS) -c -o $@
-	@echo
+	@ echo
 
-$(BUILD_DIR)/src/$(PROJECT)/test/%.o: src/test/%.cpp
+$(GTEST_OBJ): $(GTEST_SRC) | $(GTEST_BUILD_DIR)
 	$(CXX) $< $(CXXFLAGS) -c -o $@
-	@echo
+	@ echo
 
-$(BUILD_DIR)/src/$(PROJECT)/util/%.o: src/$(PROJECT)/util/%.cpp
-	$(CXX) $< $(CXXFLAGS) -c -o $@
-	@echo
-
-$(BUILD_DIR)/src/gtest/%.o: src/gtest/%.cpp
-	$(CXX) $< $(CXXFLAGS) -c -o $@
-	@echo
-
-$(BUILD_DIR)/src/$(PROJECT)/layers/%.cuo: src/$(PROJECT)/layers/%.cu
+$(LAYER_BUILD_DIR)/%.cuo: src/$(PROJECT)/layers/%.cu $(HXX_SRCS) \
+		| $(LAYER_BUILD_DIR)
 	$(CUDA_DIR)/bin/nvcc $(NVCCFLAGS) $(CUDA_ARCH) -c $< -o $@
-	@echo
+	@ echo
 
-$(BUILD_DIR)/src/$(PROJECT)/util/%.cuo: src/$(PROJECT)/util/%.cu
+$(UTIL_BUILD_DIR)/%.cuo: src/$(PROJECT)/util/%.cu | $(UTIL_BUILD_DIR)
 	$(CUDA_DIR)/bin/nvcc $(NVCCFLAGS) $(CUDA_ARCH) -c $< -o $@
-	@echo
+	@ echo
 
-$(BUILD_DIR)/tools/%.o: tools/%.cpp
+$(TOOL_BUILD_DIR)/%.o: tools/%.cpp $(PROTO_GEN_HEADER) | $(TOOL_BUILD_DIR)
 	$(CXX) $< $(CXXFLAGS) -c -o $@ $(LDFLAGS)
-	@echo
+	@ echo
 
-$(BUILD_DIR)/examples/%.o: examples/%.cpp
+$(EXAMPLE_BUILD_DIR)/%.o: examples/%.cpp $(PROTO_GEN_HEADER) \
+		| $(EXAMPLE_BUILD_DIRS)
 	$(CXX) $< $(CXXFLAGS) -c -o $@ $(LDFLAGS)
-	@echo
+	@ echo
 
-$(PROTO_GEN_PY): $(PROTO_SRCS)
-	protoc --proto_path=src --python_out=python $(PROTO_SRCS)
-	@echo
+$(BUILD_DIR)/src/$(PROJECT)/%.o: src/$(PROJECT)/%.cpp $(HXX_SRCS)
+	$(CXX) $< $(CXXFLAGS) -c -o $@
+	@ echo
 
-proto: $(PROTO_GEN_CC)
+proto: $(PROTO_GEN_CC) $(PROTO_GEN_HEADER)
 
-$(PROTO_GEN_CC): $(PROTO_SRCS)
-	protoc --proto_path=src --cpp_out=src $(PROTO_SRCS)
-	mkdir -p include/$(PROJECT)/proto
-	cp $(PROTO_GEN_HEADER) include/$(PROJECT)/proto/
-	@echo
+$(PROTO_BUILD_DIR)/%.pb.cc $(PROTO_BUILD_DIR)/%.pb.h : \
+		$(PROTO_SRC_DIR)/%.proto | $(PROTO_BUILD_DIR)
+	protoc --proto_path=src --cpp_out=build/src $<
+	@ echo
+
+$(PY_PROTO_BUILD_DIR)/%_pb2.py : $(PROTO_SRC_DIR)/%.proto \
+		$(PY_PROTO_INIT) | $(PY_PROTO_BUILD_DIR)
+	protoc --proto_path=src --python_out=python $<
+	@ echo
+
+$(PY_PROTO_INIT): | $(PY_PROTO_BUILD_DIR)
+	touch $(PY_PROTO_INIT)
 
 clean:
-	@- $(RM) $(NAME) $(STATIC_NAME)
-	@- $(RM) $(PROTO_GEN_HEADER) $(PROTO_GEN_CC) $(PROTO_GEN_PY)
-	@- $(RM) include/$(PROJECT)/proto/$(PROJECT).pb.h
-	@- $(RM) python/$(PROJECT)/proto/$(PROJECT)_pb2.py
-	@- $(RM) python/$(PROJECT)/*.so
-	@- $(RM) -rf $(BUILD_DIR)
+	@- $(RM) -rf $(ALL_BUILD_DIRS)
 	@- $(RM) -rf $(DISTRIBUTE_DIR)
-
-distribute: all
-	mkdir $(DISTRIBUTE_DIR)
+	@- $(RM) $(PY$(PROJECT)_SO)
+	@- $(RM) $(MAT$(PROJECT)_SO)
+
+supercleanfiles:
+	$(eval SUPERCLEAN_FILES := $(strip \
+			$(foreach ext,$(SUPERCLEAN_EXTS), $(shell find . -name '*$(ext)' \
+			-not -path './data/*'))))
+
+supercleanlist: supercleanfiles
+	@ \
+	if [ -z "$(SUPERCLEAN_FILES)" ]; then \
+	  echo "No generated files found."; \
+	else \
+	  echo $(SUPERCLEAN_FILES) | tr ' ' '\n'; \
+	fi
+
+superclean: clean supercleanfiles
+	@ \
+	if [ -z "$(SUPERCLEAN_FILES)" ]; then \
+	  echo "No generated files found."; \
+	else \
+	  echo "Deleting the following generated files:"; \
+	  echo $(SUPERCLEAN_FILES) | tr ' ' '\n'; \
+	  $(RM) $(SUPERCLEAN_FILES); \
+	fi
+
+$(DIST_ALIASES): $(DISTRIBUTE_DIR)
+
+$(DISTRIBUTE_DIR): all py $(HXX_SRCS) | $(DISTRIBUTE_SUBDIRS)
 	# add include
 	cp -r include $(DISTRIBUTE_DIR)/
 	# add tool and example binaries
-	mkdir $(DISTRIBUTE_DIR)/bin
 	cp $(TOOL_BINS) $(DISTRIBUTE_DIR)/bin
 	cp $(EXAMPLE_BINS) $(DISTRIBUTE_DIR)/bin
 	# add libraries
-	mkdir $(DISTRIBUTE_DIR)/lib
 	cp $(NAME) $(DISTRIBUTE_DIR)/lib
 	cp $(STATIC_NAME) $(DISTRIBUTE_DIR)/lib
 	# add python - it's not the standard way, indeed...
diff --git a/Makefile.config.example b/Makefile.config.example
index e747d2a76ad..09aea6f94eb 100644
--- a/Makefile.config.example
+++ b/Makefile.config.example
@@ -48,3 +48,6 @@ DISTRIBUTE_DIR := distribute
 
 # uncomment for debugging
 #DEBUG := 1
+
+# The ID of the GPU that 'make runtest' will use to run unit tests.
+TEST_GPUID := 0
diff --git a/python/caffe/proto/__init__.py b/python/caffe/proto/__init__.py
deleted file mode 100644
index e69de29bb2d..00000000000