diff --git a/CMakeLists.txt b/CMakeLists.txt
index c11d61bef6..5645f24ea4 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -99,12 +99,9 @@
 #
 #=============================================================================
 
-# check submodules before we do anything
-execute_process(COMMAND Tools/check_submodules.sh WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
-
 # Warning: Changing this modifies CMake's internal workings
 # and leads to wrong toolchain detection
-cmake_minimum_required(VERSION 3.1 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.2 FATAL_ERROR)
 
 set(PX4_SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}")
 set(PX4_BINARY_DIR "${CMAKE_CURRENT_BINARY_DIR}")
@@ -187,23 +184,24 @@ execute_process(
 	)
 
 px4_add_git_submodule(TARGET git_cmake_hexagon PATH "cmake/cmake_hexagon")
-px4_add_git_submodule(TARGET git_driverframework PATH "src/lib/DriverFramework")
+px4_add_git_submodule(TARGET git_uavcan_board_ident PATH "cmake/configs/uavcan_board_ident")
 px4_add_git_submodule(TARGET git_ecl PATH "src/lib/ecl")
-px4_add_git_submodule(TARGET git_gazebo PATH "Tools/sitl_gazebo")
-px4_add_git_submodule(TARGET git_gazebo_flow PATH "Tools/sitl_gazebo/external/OpticalFlow")
-px4_add_git_submodule(TARGET git_gazebo_klt PATH "Tools/sitl_gazebo/external/OpticalFlow/external/klt_feature_tracker")
-px4_add_git_submodule(TARGET git_gps_devices PATH "src/drivers/gps/devices")
-px4_add_git_submodule(TARGET git_jmavsim PATH "Tools/jMAVSim")
 px4_add_git_submodule(TARGET git_matrix PATH "src/lib/matrix")
-px4_add_git_submodule(TARGET git_mavlink PATH "mavlink/include/mavlink/v1.0")
-px4_add_git_submodule(TARGET git_mavlink2 PATH "mavlink/include/mavlink/v2.0")
-px4_add_git_submodule(TARGET git_nuttx PATH "platforms/nuttx/NuttX/nuttx")
-px4_add_git_submodule(TARGET git_uavcan PATH "src/modules/uavcan/libuavcan")
 
 #=============================================================================
 
 message(STATUS "PX4 VERSION: ${git_tag}")
 message(STATUS "CONFIG: ${target_name}")
+message(STATUS "Build Type: ${CMAKE_BUILD_TYPE}")
+
+#=============================================================================
+# project definition
+#
+project(px4 CXX C ASM)
+
+set(package-contact "px4users@googlegroups.com")
+
+#=============================================================================
 
 # The URL for the elf file for crash logging
 if (DEFINED ENV{BUILD_URI})
@@ -214,14 +212,19 @@ endif()
 
 add_definitions(-DBUILD_URI=${BUILD_URI})
 
-# Define GNU standard installation directories
-include(GNUInstallDirs)
-
 # Setup install paths
 if (${OS} STREQUAL "posix")
+
+	# Define GNU standard installation directories
+	include(GNUInstallDirs)
+
 	if (NOT CMAKE_INSTALL_PREFIX)
 		set(CMAKE_INSTALL_PREFIX "/usr" CACHE PATH "Install path prefix" FORCE)
 	endif()
+
+	# cmake testing only on posix
+	enable_testing()
+	include(CTest)
 endif()
 
 #=============================================================================
@@ -256,13 +259,6 @@ if (CCACHE AND CCACHE_PROGRAM)
 	set_property(GLOBAL PROPERTY RULE_LAUNCH_COMPILE "${CCACHE_PROGRAM}")
 endif()
 
-#=============================================================================
-# project definition
-#
-project(px4 CXX C ASM)
-
-set(package-contact "px4users@googlegroups.com")
-
 #=============================================================================
 # find programs and packages
 #
@@ -281,12 +277,6 @@ endif()
 find_package(PythonInterp REQUIRED)
 px4_find_python_module(jinja2 REQUIRED)
 
-#=============================================================================
-# cmake testing
-#
-enable_testing()
-include(CTest)
-
 #=============================================================================
 # generate compile command database
 #
@@ -368,6 +358,8 @@ px4_generate_airframes_xml(BOARD ${BOARD})
 # DriverFramework
 #
 
+px4_add_git_submodule(TARGET git_driverframework PATH "src/lib/DriverFramework")
+
 # List the DriverFramework drivers
 if (DEFINED config_df_driver_list)
 	message("DF Drivers: ${config_df_driver_list}")
diff --git a/Tools/check_submodules.sh b/Tools/check_submodules.sh
index 5fdc26acfc..6301c4f3e8 100755
--- a/Tools/check_submodules.sh
+++ b/Tools/check_submodules.sh
@@ -34,8 +34,8 @@ then
 			echo "Continuing build with manually overridden submodule.."
 		elif [ "$user_cmd" == "u" ]
 		then
-			git submodule sync --recursive
-			git submodule update --init --recursive
+			git submodule sync --recursive -- $1
+			git submodule update --init --recursive -- $1
 			echo "Submodule fixed, continuing build.."
 		else
 			echo "Build aborted."
@@ -43,10 +43,9 @@ then
 		fi
 	fi
 else
-	echo "REINITIALIZING GIT SUBMODULES"
-	echo "no git repo found in $1/.git"
+	echo "REINITIALIZING GIT SUBMODULE $1"
 	git submodule sync --recursive -- $1;
-	git submodule update --init --recursive $1;
+	git submodule update --init --recursive -- $1;
 fi
 
 }
@@ -54,15 +53,14 @@ fi
 # If called with a path then respect $GIT_SUBMODULES_ARE_EVIL but do normal processing
 if [ "$#" != "0" ];
 then
-# called with a path then process only that path but respect $GIT_SUBMODULES_ARE_EVIL
-
+	# called with a path then process only that path but respect $GIT_SUBMODULES_ARE_EVIL
 	[ -n "$GIT_SUBMODULES_ARE_EVIL" ] && {
 		# GIT_SUBMODULES_ARE_EVIL is set, meaning user doesn't want submodules updated
 		echo "GIT_SUBMODULES_ARE_EVIL is defined - Skipping submodules $1 update."
 		exit 0
 	}
 
-	git submodule update --recursive $1
+	git submodule update --init --recursive -- $1
 
 else
 
@@ -79,4 +77,5 @@ else
 	done
 
 fi
-	exit 0
+
+exit 0
diff --git a/cmake/common/px4_git.cmake b/cmake/common/px4_git.cmake
index b0877e2773..be6f74a474 100644
--- a/cmake/common/px4_git.cmake
+++ b/cmake/common/px4_git.cmake
@@ -68,6 +68,10 @@ function(px4_add_git_submodule)
 		REQUIRED TARGET PATH
 		ARGN ${ARGN})
 
+	execute_process(COMMAND ${PX4_SOURCE_DIR}/Tools/check_submodules.sh ${PATH}
+			WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+			)
+
 	string(REPLACE "/" "_" NAME ${PATH})
 
 	add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/git_init_${NAME}.stamp
diff --git a/platforms/nuttx/NuttX/CMakeLists.txt b/platforms/nuttx/NuttX/CMakeLists.txt
index 4a14d79388..be409c7953 100644
--- a/platforms/nuttx/NuttX/CMakeLists.txt
+++ b/platforms/nuttx/NuttX/CMakeLists.txt
@@ -1,5 +1,8 @@
 cmake_minimum_required(VERSION 3.2)
 
+px4_add_git_submodule(TARGET git_nuttx PATH "nuttx")
+px4_add_git_submodule(TARGET git_nuttx_apps PATH "apps")
+
 if(NOT BOARD)
 	message(FATAL_ERROR "BOARD must be set (eg px4fmu-v2)")
 endif()
@@ -40,7 +43,7 @@ file(RELATIVE_PATH CP_SRC ${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_CURRENT_SOURCE_DIR
 add_custom_command(OUTPUT nuttx_copy.stamp
 	COMMAND ${cp_cmd} ${cp_opts} ${CP_SRC} .
 	COMMAND cmake -E touch nuttx_copy.stamp
-	DEPENDS ${copy_nuttx_files}
+	DEPENDS ${copy_nuttx_files} git_nuttx
 	COMMENT "Copying NuttX/nuttx to ${CMAKE_CURRENT_BINARY_DIR}"
 	)
 
@@ -52,7 +55,7 @@ file(RELATIVE_PATH CP_SRC ${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_CURRENT_SOURCE_DIR
 add_custom_command(OUTPUT apps_copy.stamp
 	COMMAND ${cp_cmd} ${cp_opts} ${CMAKE_CURRENT_SOURCE_DIR}/apps .
 	COMMAND cmake -E touch apps_copy.stamp
-	DEPENDS ${copy_apps_files}
+	DEPENDS ${copy_apps_files} git_nuttx_apps
 	COMMENT "Copying NuttX/apps to ${CMAKE_CURRENT_BINARY_DIR}"
 	)
 set(APPS_DIR ${PX4_BINARY_DIR}/NuttX/apps)
diff --git a/src/drivers/gps/CMakeLists.txt b/src/drivers/gps/CMakeLists.txt
index d22e084820..b027f163e4 100644
--- a/src/drivers/gps/CMakeLists.txt
+++ b/src/drivers/gps/CMakeLists.txt
@@ -30,11 +30,13 @@
 # POSSIBILITY OF SUCH DAMAGE.
 #
 ############################################################################
+
+px4_add_git_submodule(TARGET git_gps_devices PATH "devices")
+
 px4_add_module(
 	MODULE drivers__gps
 	MAIN gps
 	STACK_MAIN 1200
-	COMPILE_FLAGS
 	SRCS
 		gps.cpp
 		devices/src/gps_helper.cpp
@@ -43,5 +45,5 @@ px4_add_module(
 		devices/src/ubx.cpp
 	DEPENDS
 		platforms__common
+		git_gps_devices
 	)
-# vim: set noet ft=cmake fenc=utf-8 ff=unix :
diff --git a/src/firmware/posix/CMakeLists.txt b/src/firmware/posix/CMakeLists.txt
index bdf7c384b1..781947d34e 100644
--- a/src/firmware/posix/CMakeLists.txt
+++ b/src/firmware/posix/CMakeLists.txt
@@ -107,7 +107,9 @@ elseif ("${BOARD}" STREQUAL "bebop")
 elseif ("${BOARD}" STREQUAL "sitl")
 
 	include(./sitl_target.cmake)
-	include(./sitl_tests.cmake)
+	if(BUILD_TESTING)
+		include(./sitl_tests.cmake)
+	endif()
 
 else()
 
diff --git a/src/firmware/posix/sitl_target.cmake b/src/firmware/posix/sitl_target.cmake
index c1a3a94c41..7dcac0d9d3 100644
--- a/src/firmware/posix/sitl_target.cmake
+++ b/src/firmware/posix/sitl_target.cmake
@@ -1,6 +1,6 @@
 
 function(px4_add_sitl_app)
-px4_parse_function_args(NAME px4_add_sitl_app
+	px4_parse_function_args(NAME px4_add_sitl_app
 			ONE_VALUE APP_NAME MAIN_SRC UPLOAD_NAME
 			REQUIRED APP_NAME MAIN_SRC
 			ARGN ${ARGN}
@@ -56,11 +56,14 @@ add_custom_target(run_config
 			${config_sitl_model}
 			${PX4_SOURCE_DIR}
 			${PX4_BINARY_DIR}
-			WORKING_DIRECTORY ${SITL_WORKING_DIR}
-			USES_TERMINAL
+		WORKING_DIRECTORY ${SITL_WORKING_DIR}
+		USES_TERMINAL
 		DEPENDS px4 logs_symlink
 		)
 
+px4_add_git_submodule(TARGET git_gazebo PATH "${PX4_SOURCE_DIR}/Tools/sitl_gazebo")
+px4_add_git_submodule(TARGET git_jmavsim PATH "${PX4_SOURCE_DIR}/Tools/jMAVSim")
+
 # Add support for external project building
 include(ExternalProject)
 
@@ -70,13 +73,16 @@ ExternalProject_Add(sitl_gazebo
 	CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX}
 	BINARY_DIR ${PX4_BINARY_DIR}/build_gazebo
 	INSTALL_COMMAND ""
+	DEPENDS
+		git_gazebo
 	)
 set_target_properties(sitl_gazebo PROPERTIES EXCLUDE_FROM_ALL TRUE)
 
 ExternalProject_Add_Step(sitl_gazebo forceconfigure
 	DEPENDEES update
 	DEPENDERS configure
-	ALWAYS 1)
+	ALWAYS 1
+	)
 
 # create targets for each viewer/model/debugger combination
 set(viewers none jmavsim gazebo replay)
@@ -123,9 +129,10 @@ foreach(viewer ${viewers})
 						${model}
 						${PX4_SOURCE_DIR}
 						${PX4_BINARY_DIR}
-						WORKING_DIRECTORY ${SITL_WORKING_DIR}
-						USES_TERMINAL
-					DEPENDS logs_symlink
+					WORKING_DIRECTORY ${SITL_WORKING_DIR}
+					USES_TERMINAL
+					DEPENDS
+						logs_symlink
 					)
 			list(APPEND all_posix_vmd_make_targets ${_targ_name})
 			if (viewer STREQUAL "gazebo")
@@ -133,6 +140,8 @@ foreach(viewer ${viewers})
 				if (viewer STREQUAL "gazebo")
 					add_dependencies(${_targ_name} px4_${model})
 				endif()
+			elseif(viewer STREQUAL "jmavsim")
+				add_dependencies(${_targ_name} git_jmavsim)
 			endif()
 		endforeach()
 	endforeach()
diff --git a/src/modules/ekf2/CMakeLists.txt b/src/modules/ekf2/CMakeLists.txt
index 453ac3c113..4a69cd46fb 100644
--- a/src/modules/ekf2/CMakeLists.txt
+++ b/src/modules/ekf2/CMakeLists.txt
@@ -43,4 +43,3 @@ px4_add_module(
 		platforms__common
 		git_ecl
 	)
-# vim: set noet ft=cmake fenc=utf-8 ff=unix :
diff --git a/src/modules/mavlink/CMakeLists.txt b/src/modules/mavlink/CMakeLists.txt
index ef8cbecf7b..f98c888c85 100644
--- a/src/modules/mavlink/CMakeLists.txt
+++ b/src/modules/mavlink/CMakeLists.txt
@@ -31,7 +31,8 @@
 #
 ############################################################################
 
-include_directories(${PX4_SOURCE_DIR}/mavlink/include/mavlink)
+px4_add_git_submodule(TARGET git_mavlink PATH "${PX4_SOURCE_DIR}/mavlink/include/mavlink/v1.0")
+px4_add_git_submodule(TARGET git_mavlink2 PATH "${PX4_SOURCE_DIR}/mavlink/include/mavlink/v2.0")
 
 px4_add_module(
 	MODULE modules__mavlink
@@ -41,6 +42,8 @@ px4_add_module(
 	COMPILE_FLAGS
 		-Wno-extra-semi
 		-Wno-sign-compare # TODO: fix all sign-compare
+	INCLUDES
+		${PX4_SOURCE_DIR}/mavlink/include/mavlink
 	SRCS
 		mavlink.c
 		mavlink_command_sender.cpp
@@ -58,5 +61,6 @@ px4_add_module(
 		mavlink_ulog.cpp
 	DEPENDS
 		platforms__common
+		git_mavlink
+		git_mavlink2
 	)
-# vim: set noet ft=cmake fenc=utf-8 ff=unix :
diff --git a/src/modules/simulator/CMakeLists.txt b/src/modules/simulator/CMakeLists.txt
index 3de83e51a1..6796b0abd8 100644
--- a/src/modules/simulator/CMakeLists.txt
+++ b/src/modules/simulator/CMakeLists.txt
@@ -63,8 +63,4 @@ px4_add_module(
 		${SIMULATOR_SRCS}
 	DEPENDS
 		platforms__common
-		git_jmavsim
-		git_gazebo
 	)
-
-# vim: set noet ft=cmake fenc=utf-8 ff=unix : 
diff --git a/src/modules/uavcan/CMakeLists.txt b/src/modules/uavcan/CMakeLists.txt
index eb0fab8316..7197c45418 100644
--- a/src/modules/uavcan/CMakeLists.txt
+++ b/src/modules/uavcan/CMakeLists.txt
@@ -31,6 +31,8 @@
 #
 ############################################################################
 
+px4_add_git_submodule(TARGET git_uavcan PATH "libuavcan")
+
 set(UAVCAN_USE_CPP03 ON CACHE BOOL "uavcan cpp03")
 set(UAVCAN_PLATFORM stm32 CACHE STRING "uavcan platform")
 
@@ -50,20 +52,19 @@ add_definitions(
 		)
 
 add_subdirectory(libuavcan EXCLUDE_FROM_ALL)
-add_dependencies(uavcan platforms__nuttx)
-
-include_directories(${PX4_SOURCE_DIR}/mavlink/include/mavlink)
-include_directories(libuavcan/libuavcan/include)
-include_directories(libuavcan/libuavcan/include/dsdlc_generated)
-include_directories(libuavcan/libuavcan_drivers/posix/include)
-include_directories(libuavcan/libuavcan_drivers/stm32/driver/include)
+add_dependencies(uavcan prebuild_targets)
 
 px4_add_module(
 	MODULE modules__uavcan
 	MAIN uavcan
 	STACK_MAIN 3200
 	STACK_MAX 1500
-	COMPILE_FLAGS
+	INCLUDES
+		${PX4_SOURCE_DIR}/mavlink/include/mavlink
+		libuavcan/libuavcan/include
+		libuavcan/libuavcan/include/dsdlc_generated
+		libuavcan/libuavcan_drivers/posix/include
+		libuavcan/libuavcan_drivers/stm32/driver/include
 	SRCS
 		# Main
 		uavcan_main.cpp
@@ -81,8 +82,10 @@ px4_add_module(
 		sensors/baro.cpp
 
 	DEPENDS
+		git_uavcan
 		platforms__common
 		uavcan
+		uavcan_stm32_driver
 	)
 
 target_link_libraries(modules__uavcan uavcan uavcan_stm32_driver)