diff --git a/Makefile b/Makefile
index 2b9a34553f..e2f1814f0c 100644
--- a/Makefile
+++ b/Makefile
@@ -89,7 +89,7 @@ endif
 # --------------------------------------------------------------------
 # describe how to build a cmake config
 define cmake-build
-+@if [ ! -e $(PWD)/build_$@/CMakeCache.txt ]; then mkdir -p $(PWD)/build_$@ && cd $(PWD)/build_$@ && cmake .. -G$(PX4_CMAKE_GENERATOR) -DCONFIG=$(1); fi
++@if [ ! -e $(PWD)/build_$@/CMakeCache.txt ]; then git submodule update --init --recursive --force && mkdir -p $(PWD)/build_$@ && cd $(PWD)/build_$@ && cmake .. -G$(PX4_CMAKE_GENERATOR) -DCONFIG=$(1); fi
 +$(PX4_MAKE) -C $(PWD)/build_$@ $(PX4_MAKE_ARGS) $(ARGS)
 endef
 
@@ -104,13 +104,13 @@ endef
 # --------------------------------------------------------------------
 #  Do not put any spaces between function arguments.
 
-px4fmu-v1_default: git-init
+px4fmu-v1_default:
 	$(call cmake-build,nuttx_px4fmu-v1_default)
 
-px4fmu-v2_default: git-init
+px4fmu-v2_default:
 	$(call cmake-build,nuttx_px4fmu-v2_default)
 
-px4fmu-v2_simple: git-init
+px4fmu-v2_simple:
 	$(call cmake-build,nuttx_px4fmu-v2_simple)
 
 nuttx_sim_simple:
@@ -172,19 +172,8 @@ check_format:
 
 clean:
 	@rm -rf build_*/
-
-distclean: clean
-	@cd NuttX
-	@git clean -d -f -x
-	@cd ..
-	@cd src/modules/uavcan/libuavcan
-	@git clean -d -f -x
-	@cd ../../../..
-
-# XXX this is not the right way to fix it, but we need a temporary solution
-# for average joe
-git-init:
-	@git submodule update --init --recursive
+	@(cd NuttX && git clean -d -f -x)
+	@(cd src/modules/uavcan/libuavcan && git clean -d -f -x)
 
 # targets handled by cmake
 cmake_targets = test upload package package_source debug debug_tui debug_ddd debug_io debug_io_tui debug_io_ddd check_weak libuavcan
diff --git a/Tools/check_submodules.sh b/Tools/check_submodules.sh
deleted file mode 100755
index 5fa0831438..0000000000
--- a/Tools/check_submodules.sh
+++ /dev/null
@@ -1,144 +0,0 @@
-#!/bin/sh
-
-[ -n "$GIT_SUBMODULES_ARE_EVIL" ] && {
-    # GIT_SUBMODULES_ARE_EVIL is set, meaning user doesn't want submodules
-    echo "Skipping submodules. NUTTX_SRC is set to $NUTTX_SRC"
-    exit 0
-}
-
-if [ -d NuttX/nuttx ];
-	then
-	STATUSRETVAL=$(git submodule summary | grep -A20 -i "NuttX" | grep "<")
-	if [ -z "$STATUSRETVAL" ]; then
-		echo "Checked NuttX submodule, correct version found"
-	else
-		echo ""
-		echo ""
-		echo "New commits required:"
-		echo "$(git submodule summary)"
-		echo ""
-		echo ""
-		echo "   NuttX sub repo not at correct version. Try 'git submodule update'"
-		echo "   or follow instructions on http://pixhawk.org/dev/git/submodules"
-		echo ""
-		echo "   DO NOT FORGET TO RUN 'make distclean && make archives' AFTER EACH NUTTX UPDATE!"
-		exit 1
-	fi
-else
-	git submodule update --init --recursive
-fi
-
-
-if [ -d mavlink/include/mavlink/v1.0 ];
-	then
-	STATUSRETVAL=$(git submodule summary | grep -A20 -i "mavlink/include/mavlink/v1.0" | grep "<")
-	if [ -z "$STATUSRETVAL" ]; then
-		echo "Checked mavlink submodule, correct version found"
-	else
-		echo ""
-		echo ""
-		echo "New commits required:"
-		echo "$(git submodule summary)"
-		echo ""
-		echo ""
-		echo "mavlink sub repo not at correct version. Try 'git submodule update'"
-		echo "or follow instructions on http://pixhawk.org/dev/git/submodules"
-		exit 1
-	fi
-else
-	git submodule update --init --recursive
-fi
-
-
-if [ -d uavcan ]
-then
-	STATUSRETVAL=$(git submodule summary | grep -A20 -i uavcan | grep "<")
-	if [ -z "$STATUSRETVAL" ]
-	then
-		echo "Checked uavcan submodule, correct version found"
-	else
-		echo ""
-		echo ""
-		echo "New commits required:"
-		echo "$(git submodule summary)"
-		echo ""
-		echo ""
-		echo "uavcan sub repo not at correct version. Try 'git submodule update'"
-		echo "or follow instructions on http://pixhawk.org/dev/git/submodules"
-		exit 1
-	fi
-else
-	git submodule update --init --recursive
-fi
-
-if [ -d src/lib/eigen ]
-then
-	echo "ARG = $1"
-	if [ $1 = "qurt" ]
-	then
-		# QuRT needs to use Eigen 3.2 because the toolchain doews not support C++11
-		STATUSRETVAL=$(true)
-	else
-		STATUSRETVAL=$(git submodule summary | grep -A20 -i eigen | grep "<")
-		if [ -z "$STATUSRETVAL" ]
-		then
-			echo "Checked Eigen submodule, correct version found"
-		else
-			echo ""
-			echo ""
-			echo "New commits required:"
-			echo "$(git submodule summary)"
-			echo ""
-			echo ""
-			echo "eigen sub repo not at correct version. Try 'git submodule update'"
-			echo "or follow instructions on http://pixhawk.org/dev/git/submodules"
-			exit 1
-		fi
-	fi
-else
-	git submodule update --init --recursive
-fi
-
-if [ -d Tools/gencpp ]
-then
-	STATUSRETVAL=$(git submodule summary | grep -A20 -i gencpp | grep "<")
-	if [ -z "$STATUSRETVAL" ]
-	then
-		echo "Checked gencpp submodule, correct version found"
-	else
-		echo ""
-		echo ""
-		echo "New commits required:"
-		echo "$(git submodule summary)"
-		echo ""
-		echo ""
-		echo "gencpp sub repo not at correct version. Try 'git submodule update'"
-		echo "or follow instructions on http://pixhawk.org/dev/git/submodules"
-		exit 1
-	fi
-else
-	git submodule update --init --recursive
-fi
-
-if [ -d Tools/genmsg ]
-then
-	STATUSRETVAL=$(git submodule summary | grep -A20 -i genmsg | grep "<")
-	if [ -z "$STATUSRETVAL" ]
-	then
-		echo "Checked genmsg submodule, correct version found"
-	else
-		echo ""
-		echo ""
-		echo "New commits required:"
-		echo "$(git submodule summary)"
-		echo ""
-		echo ""
-		echo "genmsg sub repo not at correct version. Try 'git submodule update'"
-		echo "or follow instructions on http://pixhawk.org/dev/git/submodules"
-		exit 1
-	fi
-else
-	git submodule update --init --recursive
-fi
-
-exit 0
diff --git a/cmake/common/px4_base.cmake b/cmake/common/px4_base.cmake
index 9a0b17b7a2..086f77070f 100644
--- a/cmake/common/px4_base.cmake
+++ b/cmake/common/px4_base.cmake
@@ -136,14 +136,17 @@ function(px4_add_git_submodule)
 		REQUIRED TARGET PATH
 		ARGN ${ARGN})
 	string(REPLACE "/" "_" NAME ${PATH})
-	add_custom_command(OUTPUT ${CMAKE_BINARY_DIR}/git_${NAME}.stamp
+	add_custom_command(OUTPUT ${CMAKE_BINARY_DIR}/git_init_${NAME}.stamp
 		WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
-		COMMAND git submodule update --init --recursive -f ${PATH}
-		COMMAND touch ${CMAKE_BINARY_DIR}/git_${NAME}.stamp
+		COMMAND git submodule init ${PATH}
+		COMMAND touch ${CMAKE_BINARY_DIR}/git_init_${NAME}.stamp
+		DEPENDS ${CMAKE_SOURCE_DIR}/.gitmodules
 		)
 	add_custom_target(${TARGET}
-		DEPENDS git_${NAME}.stamp
-	)
+		WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+		COMMAND git submodule update --recursive ${PATH}
+		DEPENDS ${CMAKE_BINARY_DIR}/git_init_${NAME}.stamp
+		)
 endfunction()
 
 #=============================================================================
@@ -543,6 +546,7 @@ function(px4_add_common_flags)
 	endif()
 
 	set(c_warnings
+		-Wbad-function-cast
 		-Wstrict-prototypes
 		-Wmissing-prototypes
 		-Wnested-externs
diff --git a/cmake/nuttx/px4_impl_nuttx.cmake b/cmake/nuttx/px4_impl_nuttx.cmake
index 2586478383..af7391f45c 100644
--- a/cmake/nuttx/px4_impl_nuttx.cmake
+++ b/cmake/nuttx/px4_impl_nuttx.cmake
@@ -213,8 +213,8 @@ function(px4_nuttx_add_export)
 	# copy
 	add_custom_command(OUTPUT nuttx_copy_${CONFIG}.stamp
 		COMMAND ${MKDIR} -p ${CMAKE_BINARY_DIR}/${CONFIG}
-		COMMAND ${RM} -rf ${nuttx_src}
-		COMMAND ${CP} -r ${CMAKE_SOURCE_DIR}/NuttX ${nuttx_src}
+		COMMAND ${MKDIR} -p ${nuttx_src}
+		COMMAND ${CP} -a ${CMAKE_SOURCE_DIR}/NuttX/. ${nuttx_src}/
 		COMMAND ${RM} -rf ${nuttx_src}/.git
 		COMMAND ${TOUCH} nuttx_copy_${CONFIG}.stamp
 		DEPENDS ${DEPENDS})
@@ -229,7 +229,7 @@ function(px4_nuttx_add_export)
 		COMMAND ${CP} -r ${CMAKE_SOURCE_DIR}/nuttx-configs/${CONFIG} ${nuttx_src}/nuttx/configs
 		COMMAND cd ${nuttx_src}/nuttx/tools && ./configure.sh ${CONFIG}/nsh
 		COMMAND ${ECHO} Exporting NuttX for ${CONFIG}
-		COMMAND ${MAKE} --no-print-directory --quiet -C ${nuttx_src}/nuttx -j${THREADS} -r CONFIG_ARCH_BOARD=${CONFIG} export
+		COMMAND ${MAKE} --no-print-directory --quiet -C ${nuttx_src}/nuttx -j${THREADS} -r CONFIG_ARCH_BOARD=${CONFIG} export > /dev/null
 		COMMAND ${CP} -r ${nuttx_src}/nuttx/nuttx-export.zip ${CMAKE_BINARY_DIR}/${CONFIG}.export
 		DEPENDS ${config_files} ${DEPENDS} __nuttx_copy_${CONFIG})
 
diff --git a/src/modules/uavcan/CMakeLists.txt b/src/modules/uavcan/CMakeLists.txt
index c2bf52247d..b8c899840a 100644
--- a/src/modules/uavcan/CMakeLists.txt
+++ b/src/modules/uavcan/CMakeLists.txt
@@ -81,7 +81,7 @@ px4_add_module(
 
 	DEPENDS
 		platforms__common
-		uavcan	
+		uavcan
 	)
 
 ## vim: set noet ft=cmake fenc=utf-8 ff=unix :