diff --git a/APMrover2/Makefile b/APMrover2/Makefile
deleted file mode 100644
index 2e0171e706..0000000000
--- a/APMrover2/Makefile
+++ /dev/null
@@ -1 +0,0 @@
-include ../mk/apm.mk
diff --git a/APMrover2/make.inc b/APMrover2/make.inc
deleted file mode 100644
index 9445d466d3..0000000000
--- a/APMrover2/make.inc
+++ /dev/null
@@ -1,54 +0,0 @@
-LIBRARIES = AP_Common
-LIBRARIES += AP_Param
-LIBRARIES += StorageManager
-LIBRARIES += AP_GPS
-LIBRARIES += AP_Baro
-LIBRARIES += AP_Compass
-LIBRARIES += AP_Math
-LIBRARIES += AP_InertialSensor
-LIBRARIES += AP_AccelCal
-LIBRARIES += AP_AHRS
-LIBRARIES += AP_NavEKF2
-LIBRARIES += AP_NavEKF3
-LIBRARIES += AP_Mission
-LIBRARIES += AP_Rally
-LIBRARIES += AP_Terrain
-LIBRARIES += RC_Channel
-LIBRARIES += AP_RangeFinder
-LIBRARIES += Filter
-LIBRARIES += Butter
-LIBRARIES += AP_Buffer
-LIBRARIES += ModeFilter
-LIBRARIES += AverageFilter
-LIBRARIES += AP_Mount
-LIBRARIES += AP_Camera
-LIBRARIES += GCS_MAVLink
-LIBRARIES += AP_SerialManager
-LIBRARIES += AP_Vehicle
-LIBRARIES += DataFlash
-LIBRARIES += AP_RCMapper
-LIBRARIES += AP_Scheduler
-LIBRARIES += AP_Navigation
-LIBRARIES += APM_Control
-LIBRARIES += AP_L1_Control
-LIBRARIES += AP_BoardConfig
-LIBRARIES += AP_Frsky_Telem
-LIBRARIES += AP_Notify
-LIBRARIES += AP_BattMonitor
-LIBRARIES += AP_OpticalFlow
-LIBRARIES += AP_Declination
-LIBRARIES += AP_RPM
-LIBRARIES += AP_Arming
-LIBRARIES += AP_Stats
-LIBRARIES += AP_Beacon
-LIBRARIES += AP_WheelEncoder
-LIBRARIES += AP_AdvancedFailsafe
-LIBRARIES += AR_AttitudeControl
-LIBRARIES += AC_PID
-LIBRARIES += AC_Fence
-LIBRARIES += AP_SmartRTL
-LIBRARIES += AC_AttitudeControl
-LIBRARIES += AP_Devo_Telem
-LIBRARIES += AP_Follow
-LIBRARIES += AP_OSD
-LIBRARIES += AP_WindVane
diff --git a/AntennaTracker/Makefile b/AntennaTracker/Makefile
deleted file mode 100644
index 2e0171e706..0000000000
--- a/AntennaTracker/Makefile
+++ /dev/null
@@ -1 +0,0 @@
-include ../mk/apm.mk
diff --git a/AntennaTracker/make.inc b/AntennaTracker/make.inc
deleted file mode 100644
index 88a45563c8..0000000000
--- a/AntennaTracker/make.inc
+++ /dev/null
@@ -1,34 +0,0 @@
-LIBRARIES += AP_Common
-LIBRARIES += AP_Param
-LIBRARIES += StorageManager
-LIBRARIES += AP_GPS
-LIBRARIES += AP_Baro
-LIBRARIES += AP_Compass
-LIBRARIES += AP_Math
-LIBRARIES += AP_AccelCal
-LIBRARIES += AP_InertialSensor
-LIBRARIES += AP_AHRS
-LIBRARIES += Filter
-LIBRARIES += AP_Buffer
-LIBRARIES += GCS_MAVLink
-LIBRARIES += AP_SerialManager
-LIBRARIES += AP_Declination
-LIBRARIES += DataFlash
-LIBRARIES += AC_PID
-LIBRARIES += AP_Scheduler
-LIBRARIES += AP_NavEKF2
-LIBRARIES += AP_NavEKF3
-LIBRARIES += AP_Vehicle
-LIBRARIES += AP_Mission
-LIBRARIES += AP_Terrain
-LIBRARIES += AP_Rally
-LIBRARIES += AP_Notify
-LIBRARIES += AP_BattMonitor
-LIBRARIES += RC_Channel
-LIBRARIES += AP_BoardConfig
-LIBRARIES += AP_OpticalFlow
-LIBRARIES += AP_RangeFinder
-LIBRARIES += AP_Mount
-LIBRARIES += AP_RPM
-LIBRARIES += AP_Frsky_Telem
-LIBRARIES += AP_Beacon
diff --git a/ArduCopter/Makefile b/ArduCopter/Makefile
deleted file mode 100644
index 725e5d2810..0000000000
--- a/ArduCopter/Makefile
+++ /dev/null
@@ -1,2 +0,0 @@
-include ../mk/apm.mk
-
diff --git a/ArduCopter/make.inc b/ArduCopter/make.inc
deleted file mode 100644
index e875936b5e..0000000000
--- a/ArduCopter/make.inc
+++ /dev/null
@@ -1,64 +0,0 @@
-LIBRARIES += AP_Common
-LIBRARIES += AP_AdvancedFailsafe
-LIBRARIES += AP_Param
-LIBRARIES += StorageManager
-LIBRARIES += GCS
-LIBRARIES += GCS_MAVLink
-LIBRARIES += AP_SerialManager
-LIBRARIES += AP_GPS
-LIBRARIES += DataFlash
-LIBRARIES += AP_Baro
-LIBRARIES += AP_Compass
-LIBRARIES += AP_Math
-LIBRARIES += AP_InertialSensor
-LIBRARIES += AP_AccelCal
-LIBRARIES += AP_AHRS
-LIBRARIES += AP_NavEKF2
-LIBRARIES += AP_NavEKF3
-LIBRARIES += AP_Mission
-LIBRARIES += AP_Rally
-LIBRARIES += AC_PID
-LIBRARIES += AC_PI_2D
-LIBRARIES += AC_HELI_PID
-LIBRARIES += AC_P
-LIBRARIES += AC_AttitudeControl
-LIBRARIES += AC_AttitudeControl_Heli
-LIBRARIES += AC_PosControl
-LIBRARIES += RC_Channel
-LIBRARIES += AP_Motors
-LIBRARIES += AP_RangeFinder
-LIBRARIES += AP_OpticalFlow
-LIBRARIES += Filter
-LIBRARIES += AP_Buffer
-LIBRARIES += AP_Camera
-LIBRARIES += AP_Mount
-LIBRARIES += AP_Vehicle
-LIBRARIES += AP_InertialNav
-LIBRARIES += AC_WPNav
-LIBRARIES += AC_Loiter
-LIBRARIES += AC_Circle
-LIBRARIES += AP_Declination
-LIBRARIES += AC_Fence
-LIBRARIES += AP_Scheduler
-LIBRARIES += AP_RCMapper
-LIBRARIES += AP_Notify
-LIBRARIES += AP_BattMonitor
-LIBRARIES += AP_BoardConfig
-LIBRARIES += AP_Frsky_Telem
-LIBRARIES += AP_Parachute
-LIBRARIES += AP_Terrain
-LIBRARIES += AP_RPM
-LIBRARIES += AC_PrecLand
-LIBRARIES += AP_IRLock
-LIBRARIES += AC_InputManager
-LIBRARIES += AP_ADSB
-LIBRARIES += AP_Avoidance
-LIBRARIES += AP_Stats
-LIBRARIES += AP_Beacon
-LIBRARIES += AP_Arming
-LIBRARIES += AP_SmartRTL
-LIBRARIES += AP_Winch
-LIBRARIES += AP_WheelEncoder
-LIBRARIES += AP_Follow
-LIBRARIES += AP_Devo_Telem
-LIBRARIES += AP_OSD
diff --git a/ArduPlane/Makefile b/ArduPlane/Makefile
deleted file mode 100644
index 725e5d2810..0000000000
--- a/ArduPlane/Makefile
+++ /dev/null
@@ -1,2 +0,0 @@
-include ../mk/apm.mk
-
diff --git a/ArduPlane/make.inc b/ArduPlane/make.inc
deleted file mode 100644
index 4407b402bc..0000000000
--- a/ArduPlane/make.inc
+++ /dev/null
@@ -1,60 +0,0 @@
-LIBRARIES += AP_Common
-LIBRARIES += AP_Param
-LIBRARIES += StorageManager
-LIBRARIES += AP_GPS
-LIBRARIES += AP_Baro
-LIBRARIES += AP_Compass
-LIBRARIES += AP_Math
-LIBRARIES += AP_InertialSensor
-LIBRARIES += AP_AccelCal
-LIBRARIES += AP_AHRS
-LIBRARIES += RC_Channel
-LIBRARIES += AP_RangeFinder
-LIBRARIES += Filter
-LIBRARIES += AP_Buffer
-LIBRARIES += AP_Camera
-LIBRARIES += AP_Terrain
-LIBRARIES += AP_AdvancedFailsafe
-LIBRARIES += APM_Control
-LIBRARIES += AP_AutoTune
-LIBRARIES += GCS
-LIBRARIES += GCS_MAVLink
-LIBRARIES += AP_SerialManager
-LIBRARIES += AP_Mount
-LIBRARIES += AP_Declination
-LIBRARIES += DataFlash
-LIBRARIES += AP_Scheduler
-LIBRARIES += AP_Navigation
-LIBRARIES += AP_L1_Control
-LIBRARIES += AP_RCMapper
-LIBRARIES += AP_Vehicle
-LIBRARIES += AP_SpdHgtControl
-LIBRARIES += AP_TECS
-LIBRARIES += AP_NavEKF2
-LIBRARIES += AP_NavEKF3
-LIBRARIES += AP_Mission
-LIBRARIES += AP_Notify
-LIBRARIES += AP_BattMonitor
-LIBRARIES += AP_Arming
-LIBRARIES += AP_BoardConfig
-LIBRARIES += AP_Frsky_Telem
-LIBRARIES += AP_Rally
-LIBRARIES += AP_OpticalFlow
-LIBRARIES += AP_RPM
-LIBRARIES += AP_Parachute
-LIBRARIES += AP_ADSB
-LIBRARIES += AP_Avoidance
-LIBRARIES += AP_Motors
-LIBRARIES += AC_AttitudeControl
-LIBRARIES += AC_PID
-LIBRARIES += AP_InertialNav
-LIBRARIES += AC_WPNav
-LIBRARIES += AC_Fence
-LIBRARIES += AP_Tuning
-LIBRARIES += AP_Stats
-LIBRARIES += AP_Landing
-LIBRARIES += AP_Beacon
-LIBRARIES += PID
-LIBRARIES += AP_Soaring
-LIBRARIES += AP_Devo_Telem
-LIBRARIES += AP_OSD
diff --git a/ArduSub/Makefile b/ArduSub/Makefile
deleted file mode 100644
index 725e5d2810..0000000000
--- a/ArduSub/Makefile
+++ /dev/null
@@ -1,2 +0,0 @@
-include ../mk/apm.mk
-
diff --git a/ArduSub/make.inc b/ArduSub/make.inc
deleted file mode 100644
index 90af456c86..0000000000
--- a/ArduSub/make.inc
+++ /dev/null
@@ -1,50 +0,0 @@
-LIBRARIES += AP_Common
-LIBRARIES += AP_Param
-LIBRARIES += StorageManager
-LIBRARIES += GCS
-LIBRARIES += GCS_MAVLink
-LIBRARIES += AP_SerialManager
-LIBRARIES += AP_GPS
-LIBRARIES += DataFlash
-LIBRARIES += AP_Baro
-LIBRARIES += AP_Compass
-LIBRARIES += AP_Math
-LIBRARIES += AP_InertialSensor
-LIBRARIES += AP_AccelCal
-LIBRARIES += AP_AHRS
-LIBRARIES += AP_NavEKF2
-LIBRARIES += AP_NavEKF3
-LIBRARIES += AP_Mission
-LIBRARIES += AP_Rally
-LIBRARIES += AC_PID
-LIBRARIES += AC_PI_2D
-LIBRARIES += AC_P
-LIBRARIES += AC_AttitudeControl
-LIBRARIES += AC_PosControl_Sub
-LIBRARIES += RC_Channel
-LIBRARIES += AP_Motors
-LIBRARIES += AP_RangeFinder
-LIBRARIES += AP_OpticalFlow
-LIBRARIES += Filter
-LIBRARIES += AP_Camera
-LIBRARIES += AP_Mount
-LIBRARIES += AP_Vehicle
-LIBRARIES += AP_InertialNav
-LIBRARIES += AC_WPNav
-LIBRARIES += AC_Loiter
-LIBRARIES += AC_Circle
-LIBRARIES += AP_Declination
-LIBRARIES += AC_Fence
-LIBRARIES += AP_Scheduler
-LIBRARIES += AP_RCMapper
-LIBRARIES += AP_Notify
-LIBRARIES += AP_BattMonitor
-LIBRARIES += AP_BoardConfig
-LIBRARIES += AP_Frsky_Telem
-LIBRARIES += AP_Terrain
-LIBRARIES += AP_RPM
-LIBRARIES += AP_JSButton
-LIBRARIES += AP_LeakDetector
-LIBRARIES += AP_Beacon
-LIBRARIES += AP_TemperatureSensor
-LIBRARIES += AP_Arming
diff --git a/Makefile b/Makefile
index 9471ef452d..1240e7c4c7 100644
--- a/Makefile
+++ b/Makefile
@@ -1,30 +1,89 @@
-# top level makefile to build SITL for primary vehicle targets. 
-# Useful for static analysis tools
+ROOT = $(dir $(lastword $(MAKEFILE_LIST)))
 
-all: sitl
+WAF_BINARY = $(realpath $(ROOT)/modules/waf/waf-light)
+WAF = $(WAF_BINARY) $(WAF_FLAGS)
 
-sitl: TARGET=sitl
-sitl: plane copter rover sub antennatracker
+EXPLICIT_COMMANDS = check check-all clean list_boards
 
-linux: TARGET=linux
-linux: plane copter rover sub antennatracker
+VEHICLES = copter plane rover
 
-clean: TARGET=clean
-clean: plane copter rover sub antennatracker
+all: $(WAF_BINARY)
+	@$(WAF) build
 
-.PHONY: plane copter rover sub antennatracker
+$(WAF_BINARY):
+	@git submodule init && git submodule update
 
-plane:
-	$(MAKE) -C ArduPlane $(TARGET)
+waf-%: $(WAF_BINARY)
+	@$(WAF) $*
 
-copter:
-	$(MAKE) -C ArduCopter $(TARGET)
+%-configure: $(WAF_BINARY)
+	@$(WAF) configure --board $*
 
-rover:
-	$(MAKE) -C APMrover2 $(TARGET)
+$(EXPLICIT_COMMANDS): $(WAF_BINARY)
+	@$(WAF) $@
 
-sub:
-	$(MAKE) -C ArduSub $(TARGET)
+$(VEHICLES): $(WAF_BINARY)
+	@echo Build for vehicle $@
+	@$(WAF) $@
 
-antennatracker:
-	$(MAKE) -C AntennaTracker $(TARGET)
+.DEFAULT: %-configure
+	@$(WAF) configure --board $@ build
+
+help:
+	@echo "Ardupilot Building"
+	@echo "=================="
+	@echo "This is a make wrapper for Ardupilot's Waf build system. This wrapper is"
+	@echo "intended to provide convenience for basic and common build tasks. If you need"
+	@echo "more than what this wrapper provides, it's a good idea to use waf directly."
+	@echo "The waf executable is at '$(WAF_BINARY)'."
+	@echo ""
+	@echo "WARNING: Ardupilot's Waf build system is still a work in progress, it's still"
+	@echo "missing features from the current official build system."
+	@echo ""
+	@echo "Note: The examples in this help consider this wrapper being named as Makefile"
+	@echo "or makefile. In a Linux environment, alias make='make -f THIS_MAKEFILE'"
+	@echo "should make them work."
+	@echo ""
+	@echo "Boards"
+	@echo "------"
+	@echo "In order to trigger the build for a board/platform, the name of the board is"
+	@echo "used as the target. Example: make linux"
+	@echo "If no target is passed, then the build will be triggered for the last board"
+	@echo "used. You can suffix the board/platform with '-configure' in order to just "
+	@echo "configure without triggering a build command."
+	@echo ""
+	@echo "Vehicles"
+	@echo "--------"
+	@echo "It's possible to build for a specific vehicle by defining the target as one of:"
+	@echo "    $(VEHICLES)"
+	@echo ""
+	@echo "Not that if it's your first time building or you want to change the target "
+	@echo "board/platform, you'll need to configure the build before (e.g"
+	@echo "make linux-configure)"
+	@echo ""
+	@echo "Check"
+	@echo "-----"
+	@echo "Check targets are used for running tests. There are two targets available:"
+	@echo "    check:     for running tests that are still failing or that are new or"
+	@echo "               have been modified"
+	@echo "    check-all: to run all tests"
+	@echo ""
+	@echo "Waf commands"
+	@echo "------------"
+	@echo "Waf commands can be explicitly called with targets prefixed by 'waf-'. Example:"
+	@echo "    make waf-clean"
+	@echo "    make waf-build"
+	@echo ""
+	@echo "Common commands"
+	@echo "---------------"
+	@echo "Some Waf commands can be executed without the need of prefixing the target name"
+	@echo "with 'waf-'. They are: $(EXPLICIT_COMMANDS)"
+	@echo ""
+	@echo "Waf flags"
+	@echo "---------"
+	@echo "The variable WAF_FLAGS can be used to set any waf command line options that"
+	@echo "come to be necessary. Ex: make linux WAF_FLAGS='-c no'"
+	@echo ""
+
+# Don't run in parallel, let waf take care of that.
+.NOTPARALLEL:
diff --git a/Makefile.waf b/Makefile.waf
deleted file mode 100644
index 1240e7c4c7..0000000000
--- a/Makefile.waf
+++ /dev/null
@@ -1,89 +0,0 @@
-ROOT = $(dir $(lastword $(MAKEFILE_LIST)))
-
-WAF_BINARY = $(realpath $(ROOT)/modules/waf/waf-light)
-WAF = $(WAF_BINARY) $(WAF_FLAGS)
-
-EXPLICIT_COMMANDS = check check-all clean list_boards
-
-VEHICLES = copter plane rover
-
-all: $(WAF_BINARY)
-	@$(WAF) build
-
-$(WAF_BINARY):
-	@git submodule init && git submodule update
-
-waf-%: $(WAF_BINARY)
-	@$(WAF) $*
-
-%-configure: $(WAF_BINARY)
-	@$(WAF) configure --board $*
-
-$(EXPLICIT_COMMANDS): $(WAF_BINARY)
-	@$(WAF) $@
-
-$(VEHICLES): $(WAF_BINARY)
-	@echo Build for vehicle $@
-	@$(WAF) $@
-
-.DEFAULT: %-configure
-	@$(WAF) configure --board $@ build
-
-help:
-	@echo "Ardupilot Building"
-	@echo "=================="
-	@echo "This is a make wrapper for Ardupilot's Waf build system. This wrapper is"
-	@echo "intended to provide convenience for basic and common build tasks. If you need"
-	@echo "more than what this wrapper provides, it's a good idea to use waf directly."
-	@echo "The waf executable is at '$(WAF_BINARY)'."
-	@echo ""
-	@echo "WARNING: Ardupilot's Waf build system is still a work in progress, it's still"
-	@echo "missing features from the current official build system."
-	@echo ""
-	@echo "Note: The examples in this help consider this wrapper being named as Makefile"
-	@echo "or makefile. In a Linux environment, alias make='make -f THIS_MAKEFILE'"
-	@echo "should make them work."
-	@echo ""
-	@echo "Boards"
-	@echo "------"
-	@echo "In order to trigger the build for a board/platform, the name of the board is"
-	@echo "used as the target. Example: make linux"
-	@echo "If no target is passed, then the build will be triggered for the last board"
-	@echo "used. You can suffix the board/platform with '-configure' in order to just "
-	@echo "configure without triggering a build command."
-	@echo ""
-	@echo "Vehicles"
-	@echo "--------"
-	@echo "It's possible to build for a specific vehicle by defining the target as one of:"
-	@echo "    $(VEHICLES)"
-	@echo ""
-	@echo "Not that if it's your first time building or you want to change the target "
-	@echo "board/platform, you'll need to configure the build before (e.g"
-	@echo "make linux-configure)"
-	@echo ""
-	@echo "Check"
-	@echo "-----"
-	@echo "Check targets are used for running tests. There are two targets available:"
-	@echo "    check:     for running tests that are still failing or that are new or"
-	@echo "               have been modified"
-	@echo "    check-all: to run all tests"
-	@echo ""
-	@echo "Waf commands"
-	@echo "------------"
-	@echo "Waf commands can be explicitly called with targets prefixed by 'waf-'. Example:"
-	@echo "    make waf-clean"
-	@echo "    make waf-build"
-	@echo ""
-	@echo "Common commands"
-	@echo "---------------"
-	@echo "Some Waf commands can be executed without the need of prefixing the target name"
-	@echo "with 'waf-'. They are: $(EXPLICIT_COMMANDS)"
-	@echo ""
-	@echo "Waf flags"
-	@echo "---------"
-	@echo "The variable WAF_FLAGS can be used to set any waf command line options that"
-	@echo "come to be necessary. Ex: make linux WAF_FLAGS='-c no'"
-	@echo ""
-
-# Don't run in parallel, let waf take care of that.
-.NOTPARALLEL:
diff --git a/mk/PX4/.gitignore b/mk/PX4/.gitignore
deleted file mode 100644
index 6887fd3c93..0000000000
--- a/mk/PX4/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-!*.d
diff --git a/mk/PX4/ROMFS/bootloader/README.txt b/mk/PX4/ROMFS/bootloader/README.txt
deleted file mode 100644
index f132c3b593..0000000000
--- a/mk/PX4/ROMFS/bootloader/README.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-bootloaders for PX4 build are now in Tools/bootloaders/
-
diff --git a/mk/PX4/ROMFS/init.d/rc.APM b/mk/PX4/ROMFS/init.d/rc.APM
deleted file mode 100755
index c7bc5f3e76..0000000000
--- a/mk/PX4/ROMFS/init.d/rc.APM
+++ /dev/null
@@ -1,48 +0,0 @@
-#!nsh
-
-# APM startup script for NuttX on PX4
-
-# To disable APM startup add a /fs/microsd/APM/nostart file
-
-# check for an old file called APM, caused by 
-# a bug in an earlier firmware release
-if [ -f /fs/microsd/APM ]
-then
-    echo "APM file found - renaming"
-    mv /fs/microsd/APM /fs/microsd/APM.old
-fi
-
-if [ -f /fs/microsd/APM/nostart ]
-then
-    echo "APM/nostart found - skipping APM startup"
-    sh /etc/init.d/rc.error
-fi
-
-set sketch NONE
-if rm /fs/microsd/APM/boot.log
-then
-    echo "removed old boot.log"
-fi
-set logfile /fs/microsd/APM/BOOT.LOG
-
-if mkdir /fs/microsd/APM > /dev/null
-then
-    echo "Created APM directory"
-fi
-
-if uorb start
-then
-    echo "uorb started OK"
-else
-    sh /etc/init.d/rc.error
-fi
-
-echo Starting ArduPilot
-if ArduPilot start
-then
-    echo ArduPilot started OK
-else
-    sh /etc/init.d/rc.error
-fi
-
-echo "rc.APM finished"
diff --git a/mk/PX4/ROMFS/init.d/rc.aerofc-v1 b/mk/PX4/ROMFS/init.d/rc.aerofc-v1
deleted file mode 100644
index 33210c26b4..0000000000
--- a/mk/PX4/ROMFS/init.d/rc.aerofc-v1
+++ /dev/null
@@ -1,5 +0,0 @@
-# AEROFC-V1 custom definitions
-
-set NSH_ERROR_UART1 /dev/ttyS4
-set NSH_ERROR_UART2 none
-set USB none
diff --git a/mk/PX4/ROMFS/init.d/rc.error b/mk/PX4/ROMFS/init.d/rc.error
deleted file mode 100644
index 92ba8b13a2..0000000000
--- a/mk/PX4/ROMFS/init.d/rc.error
+++ /dev/null
@@ -1,19 +0,0 @@
-echo "Error in startup"
-
-if [ $HAVE_RGBLED == 1 ]
-then
-        rgbled rgb 16 0 0
-fi
-
-if [ $NSH_ERROR_UART1 != none ]
-then
-	nshterm $NSH_ERROR_UART1 &
-	sleep 1
-fi
-if [ $NSH_ERROR_UART2 != none ]
-then
-	nshterm $NSH_ERROR_UART2 &
-	sleep 1
-fi
-
-exit
diff --git a/mk/PX4/ROMFS/init.d/rcS b/mk/PX4/ROMFS/init.d/rcS
deleted file mode 100755
index 44d99c5816..0000000000
--- a/mk/PX4/ROMFS/init.d/rcS
+++ /dev/null
@@ -1,77 +0,0 @@
-#!nsh
-#
-# PX4FMU startup script.
-#
-# This script is responsible for:
-#
-# - mounting the microSD card (if present)
-# - running the user startup script from the microSD card (if present)
-# - detecting the configuration of the system and picking a suitable
-#   startup script to continue with
-#
-# Note: DO NOT add configuration-specific commands to this script;
-#       add them to the per-configuration scripts instead.
-#
-
-set USB autoconnect
-set NSH_ERROR_UART1 /dev/ttyACM0
-set NSH_ERROR_UART2 /dev/ttyS0
-
-#
-# Try to mount the microSD card.
-#
-echo "[init] looking for microSD..."
-if mount -t vfat /dev/mmcsd0 /fs/microsd
-then
-    echo "[init] card mounted at /fs/microsd"
-fi
-
-# Look for an additional init script that allows changing the default
-# behavior. Settings may be overriden in the following order:
-#
-# board-specific file
-# etc/rc on microSD card
-# etc/rc.txt on microSD card
-if [ -f /etc/init.d/rc.board ]
-then
-    echo "[init] reading /etc/init.d/rc.board"
-    sh /etc/init.d/rc.board
-fi
-if [ -f /fs/microsd/etc/rc ]
-then
-    echo "[init] reading /fs/microsd/etc/rc"
-    sh /fs/microsd/etc/rc
-fi
-# Also consider rc.txt files
-if [ -f /fs/microsd/etc/rc.txt ]
-then
-    echo "[init] reading /fs/microsd/etc/rc.txt"
-    sh /fs/microsd/etc/rc.txt
-fi
-
-#
-# Check for USB host
-#
-if [ $USB != autoconnect ]
-then
-    echo "[init] not connecting USB"
-else
-    if sercon
-    then
-        echo "[init] USB interface connected"
-    else
-        echo "[init] No USB connected"
-    fi
-fi
-
-# if this is an APM build then there will be a rc.APM script
-# from an EXTERNAL_SCRIPTS build option
-if [ -f /etc/init.d/rc.APM -a ! -f /fs/microsd/APM/nostart ]
-then
-    echo Running rc.APM
-    # if APM startup is successful then nsh will exit
-    sh /etc/init.d/rc.APM
-else
-    echo "Opening USB nsh"
-    nshterm /dev/ttyACM0 &
-fi
diff --git a/mk/PX4/ROMFS/init.d/rcS_no_microSD b/mk/PX4/ROMFS/init.d/rcS_no_microSD
deleted file mode 100644
index 8ac04655d3..0000000000
--- a/mk/PX4/ROMFS/init.d/rcS_no_microSD
+++ /dev/null
@@ -1,14 +0,0 @@
-#!nsh
-set USB autoconnect
-set NSH_ERROR_UART1 /dev/ttyACM0
-set NSH_ERROR_UART2 /dev/ttyS0
-
-if sercon
-then
-    echo "[init] USB interface connected"
-else
-    echo "[init] No USB connected"
-fi
-
-echo Running rc.APM
-sh /etc/init.d/rc.APM
diff --git a/mk/PX4/ROMFS/tones/startup b/mk/PX4/ROMFS/tones/startup
deleted file mode 100644
index 0b3c3c3cc2..0000000000
--- a/mk/PX4/ROMFS/tones/startup
+++ /dev/null
@@ -1 +0,0 @@
-MFT240L8O4aO5dcO4aO5dcO4aO5dcL16dcdcdcdc
diff --git a/mk/PX4/config_px4fmu-v1_APM.mk b/mk/PX4/config_px4fmu-v1_APM.mk
deleted file mode 100644
index 19232bdd1a..0000000000
--- a/mk/PX4/config_px4fmu-v1_APM.mk
+++ /dev/null
@@ -1,7 +0,0 @@
-#
-# Makefile for the px4fmu-v1_APM configuration
-#
-include $(SKETCHBOOK)/mk/PX4/px4_common.mk
-
-MODULES		+= drivers/boards/px4fmu-v1
-MODULES		+= drivers/px4io
diff --git a/mk/PX4/config_px4fmu-v2_APM.mk b/mk/PX4/config_px4fmu-v2_APM.mk
deleted file mode 100644
index db9c3feaf3..0000000000
--- a/mk/PX4/config_px4fmu-v2_APM.mk
+++ /dev/null
@@ -1,9 +0,0 @@
-#
-# Makefile for the px4fmu-v2_APM configuration
-#
-include $(SKETCHBOOK)/mk/PX4/px4_common.mk
-
-MODULES		+= drivers/boards/px4fmu-v2
-MODULES		+= drivers/pwm_input
-MODULES		+= drivers/px4io
-
diff --git a/mk/PX4/config_px4fmu-v3_APM.mk b/mk/PX4/config_px4fmu-v3_APM.mk
deleted file mode 100644
index 93c7366854..0000000000
--- a/mk/PX4/config_px4fmu-v3_APM.mk
+++ /dev/null
@@ -1,9 +0,0 @@
-#
-# Makefile for the px4fmu-v2_APM configuration
-#
-include $(SKETCHBOOK)/mk/PX4/px4_common.mk
-
-MODULES		+= drivers/boards/px4fmu-v2
-MODULES		+= drivers/pwm_input
-MODULES		+= drivers/px4io
-MODULES		+= drivers/oreoled
diff --git a/mk/PX4/config_px4fmu-v4_APM.mk b/mk/PX4/config_px4fmu-v4_APM.mk
deleted file mode 100644
index 6d8d879e24..0000000000
--- a/mk/PX4/config_px4fmu-v4_APM.mk
+++ /dev/null
@@ -1,7 +0,0 @@
-#
-# Makefile for the px4fmu-v4_APM configuration
-#
-include $(SKETCHBOOK)/mk/PX4/px4_common.mk
-
-MODULES		+= drivers/boards/px4fmu-v4
-MODULES		+= drivers/pwm_input
diff --git a/mk/PX4/config_px4fmu-v4pro_APM.mk b/mk/PX4/config_px4fmu-v4pro_APM.mk
deleted file mode 100644
index fc6abd557d..0000000000
--- a/mk/PX4/config_px4fmu-v4pro_APM.mk
+++ /dev/null
@@ -1,9 +0,0 @@
-#
-# Makefile for the px4fmu-v2_APM configuration
-#
-include $(SKETCHBOOK)/mk/PX4/px4_common.mk
-
-MODULES		+= drivers/boards/px4fmu-v4pro
-MODULES		+= drivers/pwm_input
-MODULES		+= drivers/px4io
-
diff --git a/mk/PX4/px4_common.mk b/mk/PX4/px4_common.mk
deleted file mode 100644
index 689a8ae667..0000000000
--- a/mk/PX4/px4_common.mk
+++ /dev/null
@@ -1,74 +0,0 @@
-#
-# common makefile elements for all PX4 boards
-#
-
-#
-# Use the configuration's ROMFS.
-#
-ROMFS_ROOT	 = $(SKETCHBOOK)/mk/PX4/ROMFS
-MODULES		+= $(APM_MODULE_DIR)
-
-#
-# Board support modules
-#
-MODULES		+= drivers/device
-MODULES		+= drivers/stm32
-MODULES		+= drivers/stm32/adc
-MODULES		+= drivers/stm32/tone_alarm
-MODULES		+= drivers/led
-MODULES		+= drivers/px4fmu
-#MODULES	+= drivers/gps
-#MODULES	+= drivers/hil
-#MODULES	+= drivers/hott_telemetry
-#MODULES	+= drivers/blinkm
-#MODULES	+= modules/sensors
-
-#
-# System commands
-#
-MODULES		+= systemcmds/bl_update
-MODULES		+= systemcmds/mixer
-MODULES		+= systemcmds/perf
-MODULES		+= systemcmds/reboot
-MODULES		+= systemcmds/top
-#MODULES	+= systemcmds/tests
-MODULES		+= systemcmds/nshterm
-MODULES         += systemcmds/mtd
-MODULES         += systemcmds/ver
-
-ifneq ($(wildcard $(PX4_ROOT)/src/systemcmds/usb_connected),)  
-MODULES         += systemcmds/usb_connected
-endif
-
-#
-# Library modules
-#
-MODULES		+= modules/systemlib
-MODULES		+= modules/systemlib/mixer
-MODULES		+= modules/uORB
-
-# Note: auth disabled to keep us under 1MB flash because of STM32 bug
-#ifneq ($(wildcard $(PX4_ROOT)/src/systemcmds/auth),)  
-#MODULES		+= systemcmds/auth
-#endif
-#ifneq ($(wildcard $(PX4_ROOT)/src/modules/libtomfastmath),)  
-#MODULES	        += modules/libtomfastmath
-#MODULES         += modules/libtomcrypt
-#endif
-
-#
-# Transitional support - add commands from the NuttX export archive.
-#
-# In general, these should move to modules over time.
-#
-# Each entry here is <command>.<priority>.<stacksize>.<entrypoint> but we use a helper macro
-# to make the table a bit more readable.
-#
-define _B
-	$(strip $1).$(or $(strip $2),SCHED_PRIORITY_DEFAULT).$(or $(strip $3),CONFIG_PTHREAD_STACK_DEFAULT).$(strip $4)
-endef
-
-#                  command                 priority                   stack  entrypoint
-BUILTIN_COMMANDS := \
-	$(call _B, sercon,                 ,                          2048,  sercon_main                ) \
-	$(call _B, serdis,                 ,                          2048,  serdis_main                )
diff --git a/mk/VRBRAIN/ROMFS/init.d/rc.APM b/mk/VRBRAIN/ROMFS/init.d/rc.APM
deleted file mode 100644
index 4cd9cb0ca0..0000000000
--- a/mk/VRBRAIN/ROMFS/init.d/rc.APM
+++ /dev/null
@@ -1,71 +0,0 @@
-#!nsh
-
-# APM startup script for NuttX on VRBRAIN
-
-# To disable APM startup add a /fs/microsd/APM/nostart file
-
-# check for an old file called APM, caused by 
-# a bug in an earlier firmware release
-if [ -f /fs/microsd/APM ]
-then
-    echo "APM file found - renaming"
-    mv /fs/microsd/APM /fs/microsd/APM.old
-fi
-
-if [ -f /fs/microsd/APM/nostart ]
-then
-    echo "APM/nostart found - skipping APM startup"
-    sh /etc/init.d/rc.error
-fi
-
-# mount binfs so we can find the built-in apps
-if [ -f /bin/reboot ]
-then
-    echo "binfs already mounted"
-else
-    echo "Mounting binfs"
-    if mount -t binfs /dev/null /bin
-    then
-            echo "binfs mounted OK"
-    else
-            sh /etc/init.d/rc.error
-    fi
-fi
-
-set sketch NONE
-if rm /fs/microsd/APM/boot.log
-then
-    echo "removed old boot.log"
-fi
-set logfile /fs/microsd/APM/BOOT.LOG
-
-if [ ! -f /bin/ArduPilot ]
-then
-    echo "/bin/ardupilot not found"
-    sh /etc/init.d/rc.error
-fi
-
-if mkdir /fs/microsd/APM > /dev/null
-then
-    echo "Created APM directory"
-fi
-
-if uorb start
-then
-    echo "uorb started OK"
-else
-    sh /etc/init.d/rc.error
-fi
-
-echo Starting ArduPilot
-if ArduPilot start
-then
-    echo ArduPilot started OK
-else
-    sh /etc/init.d/rc.error
-fi
-
-echo "Exiting from nsh shell"
-exit
-
-echo "rc.APM finished"
diff --git a/mk/VRBRAIN/ROMFS/init.d/rc.error b/mk/VRBRAIN/ROMFS/init.d/rc.error
deleted file mode 100644
index 8c82168ba5..0000000000
--- a/mk/VRBRAIN/ROMFS/init.d/rc.error
+++ /dev/null
@@ -1,21 +0,0 @@
-echo "Error in startup"
-
-tone_alarm MNCC
-
-if [ $HAVE_RGBLED == 1 ]
-then
-        rgbled rgb 16 0 0
-fi
-
-if [ $NSH_ERROR_UART1 != none ]
-then
-	nshterm $NSH_ERROR_UART1 &
-	sleep 1
-fi
-if [ $NSH_ERROR_UART2 != none ]
-then
-	nshterm $NSH_ERROR_UART2 &
-	sleep 1
-fi
-
-exit
diff --git a/mk/VRBRAIN/ROMFS/init.d/rcS b/mk/VRBRAIN/ROMFS/init.d/rcS
deleted file mode 100644
index cb2d3f349d..0000000000
--- a/mk/VRBRAIN/ROMFS/init.d/rcS
+++ /dev/null
@@ -1,98 +0,0 @@
-#!nsh
-#
-# VRBRAIN startup script.
-#
-# This script is responsible for:
-#
-# - mounting the microSD card (if present)
-# - running the user startup script from the microSD card (if present)
-# - detecting the configuration of the system and picking a suitable
-#   startup script to continue with
-#
-# Note: DO NOT add configuration-specific commands to this script;
-#       add them to the per-configuration scripts instead.
-#
-
-set USB autoconnect
-set NSH_ERROR_UART1 /dev/ttyACM0
-set NSH_ERROR_UART2 /dev/ttyS0
-
-#
-# Try to mount the microSD card.
-#
-echo "[init] looking for microSD..."
-if mount -t vfat /dev/mmcsd0 /fs/microsd
-then
-    echo "[init] card mounted at /fs/microsd"
-    set HAVE_MICROSD 1
-    # Start playing the startup tune
-    if [ -f /etc/tones/startup ]
-    then
-        tone_alarm /etc/tones/startup
-    else
-        tone_alarm 1
-    fi
-else
-    set HAVE_MICROSD 0
-    tone_alarm MNBGG
-fi
-
-# Look for an additional init script that allows changing the default
-# behavior. Settings may be overriden in the following order:
-#
-# board-specific file
-# etc/rc on microSD card
-# etc/rc.txt on microSD card
-if [ -f /etc/init.d/rc.board ]
-then
-    echo "[init] reading /etc/init.d/rc.board"
-    sh /etc/init.d/rc.board
-fi
-if [ -f /fs/microsd/etc/rc ]
-then
-    echo "[init] reading /fs/microsd/etc/rc"
-    sh /fs/microsd/etc/rc
-fi
-# Also consider rc.txt files
-if [ -f /fs/microsd/etc/rc.txt ]
-then
-    echo "[init] reading /fs/microsd/etc/rc.txt"
-    sh /fs/microsd/etc/rc.txt
-fi
-
-#
-# Check for USB host
-#
-if [ $USB != autoconnect ]
-then
-    echo "[init] not connecting USB"
-else
-    if sercon
-    then
-        echo "[init] USB interface connected"
-    else
-        echo "[init] No USB connected"
-    fi
-fi
-
-if [ $HAVE_MICROSD == 0 ]
-then
-    if usb_connected
-    then
-        echo "Opening USB nsh"
-    else
-        echo "booting with no microSD"
-        set HAVE_MICROSD 1
-    fi
-fi
-
-# if this is an APM build then there will be a rc.APM script
-# from an EXTERNAL_SCRIPTS build option
-if [ -f /etc/init.d/rc.APM -a $HAVE_MICROSD == 1 -a ! -f /fs/microsd/APM/nostart ]
-then
-    echo Running rc.APM
-    # if APM startup is successful then nsh will exit
-    sh /etc/init.d/rc.APM
-else
-    nshterm /dev/ttyACM0 &
-fi
diff --git a/mk/VRBRAIN/config_vrbrain-v51_APM.mk b/mk/VRBRAIN/config_vrbrain-v51_APM.mk
deleted file mode 100644
index 0a34db4a03..0000000000
--- a/mk/VRBRAIN/config_vrbrain-v51_APM.mk
+++ /dev/null
@@ -1,8 +0,0 @@
-#
-# Makefile for the VRBRAIN 5.1 APM configuration
-#
-include $(SKETCHBOOK)/mk/VRBRAIN/vrbrain_common.mk
-
-MODULES		+= drivers/boards/vrbrain-v51
-
-
diff --git a/mk/VRBRAIN/config_vrbrain-v52E_APM.mk b/mk/VRBRAIN/config_vrbrain-v52E_APM.mk
deleted file mode 100644
index 693663fe13..0000000000
--- a/mk/VRBRAIN/config_vrbrain-v52E_APM.mk
+++ /dev/null
@@ -1,8 +0,0 @@
-#
-# Makefile for the VRBRAIN 5.2E APM configuration
-#
-include $(SKETCHBOOK)/mk/VRBRAIN/vrbrain_common.mk
-
-MODULES		+= drivers/boards/vrbrain-v52E
-MODULES		+= drivers/pwm_input
-
diff --git a/mk/VRBRAIN/config_vrbrain-v52_APM.mk b/mk/VRBRAIN/config_vrbrain-v52_APM.mk
deleted file mode 100644
index c3e12404ae..0000000000
--- a/mk/VRBRAIN/config_vrbrain-v52_APM.mk
+++ /dev/null
@@ -1,8 +0,0 @@
-#
-# Makefile for the VRBRAIN 5.2 APM configuration
-#
-include $(SKETCHBOOK)/mk/VRBRAIN/vrbrain_common.mk
-
-MODULES		+= drivers/boards/vrbrain-v52
-MODULES		+= drivers/pwm_input
-
diff --git a/mk/VRBRAIN/config_vrbrain-v54_APM.mk b/mk/VRBRAIN/config_vrbrain-v54_APM.mk
deleted file mode 100644
index 01e25f5727..0000000000
--- a/mk/VRBRAIN/config_vrbrain-v54_APM.mk
+++ /dev/null
@@ -1,8 +0,0 @@
-#
-# Makefile for the VRBRAIN 5.4 APM configuration
-#
-include $(SKETCHBOOK)/mk/VRBRAIN/vrbrain_common.mk
-
-MODULES		+= drivers/boards/vrbrain-v54
-MODULES		+= drivers/pwm_input
-
diff --git a/mk/VRBRAIN/config_vrcore-v10_APM.mk b/mk/VRBRAIN/config_vrcore-v10_APM.mk
deleted file mode 100644
index 0b99861197..0000000000
--- a/mk/VRBRAIN/config_vrcore-v10_APM.mk
+++ /dev/null
@@ -1,8 +0,0 @@
-#
-# Makefile for the VRCORE 1.0 APM configuration
-#
-include $(SKETCHBOOK)/mk/VRBRAIN/vrbrain_common.mk
-
-MODULES		+= drivers/boards/vrcore-v10
-MODULES		+= drivers/pwm_input
-
diff --git a/mk/VRBRAIN/config_vrubrain-v51_APM.mk b/mk/VRBRAIN/config_vrubrain-v51_APM.mk
deleted file mode 100644
index a986810ad6..0000000000
--- a/mk/VRBRAIN/config_vrubrain-v51_APM.mk
+++ /dev/null
@@ -1,8 +0,0 @@
-#
-# Makefile for the VRUBRAIN 5.1 APM configuration
-#
-include $(SKETCHBOOK)/mk/VRBRAIN/vrbrain_common.mk
-
-MODULES		+= drivers/boards/vrubrain-v51
-MODULES		+= drivers/pwm_input
-
diff --git a/mk/VRBRAIN/config_vrubrain-v52_APM.mk b/mk/VRBRAIN/config_vrubrain-v52_APM.mk
deleted file mode 100644
index ee5465adf1..0000000000
--- a/mk/VRBRAIN/config_vrubrain-v52_APM.mk
+++ /dev/null
@@ -1,8 +0,0 @@
-#
-# Makefile for the VRUBRAIN 5.2 APM configuration
-#
-include $(SKETCHBOOK)/mk/VRBRAIN/vrbrain_common.mk
-
-MODULES		+= drivers/boards/vrubrain-v52
-
-
diff --git a/mk/VRBRAIN/vrbrain_common.mk b/mk/VRBRAIN/vrbrain_common.mk
deleted file mode 100644
index 691f473bdb..0000000000
--- a/mk/VRBRAIN/vrbrain_common.mk
+++ /dev/null
@@ -1,74 +0,0 @@
-#
-# common makefile elements for all PX4 boards
-#
-
-#
-# Use the configuration's ROMFS.
-#
-ROMFS_ROOT	 = $(SKETCHBOOK)/mk/VRBRAIN/ROMFS
-MODULES		+= $(APM_MODULE_DIR)
-
-#
-# Board support modules
-#
-MODULES		+= drivers/device
-MODULES		+= drivers/stm32
-MODULES		+= drivers/stm32/adc
-MODULES		+= drivers/stm32/tone_alarm
-MODULES		+= drivers/led
-MODULES		+= drivers/px4fmu
-#MODULES	+= drivers/gps
-#MODULES	+= drivers/hil
-#MODULES	+= drivers/hott_telemetry
-#MODULES	+= drivers/blinkm
-#MODULES	+= modules/sensors
-
-#
-# System commands
-#
-MODULES		+= systemcmds/bl_update
-MODULES		+= systemcmds/mixer
-MODULES		+= systemcmds/perf
-MODULES		+= systemcmds/reboot
-MODULES		+= systemcmds/top
-#MODULES	+= systemcmds/tests
-MODULES		+= systemcmds/nshterm
-MODULES         += systemcmds/mtd
-MODULES         += systemcmds/ver
-
-ifneq ($(wildcard $(PX4_ROOT)/src/systemcmds/usb_connected),)  
-MODULES         += systemcmds/usb_connected
-endif
-
-#
-# Library modules
-#
-MODULES		+= modules/systemlib
-MODULES		+= modules/systemlib/mixer
-MODULES		+= modules/uORB
-
-# Note: auth disabled to keep us under 1MB flash because of STM32 bug
-#ifneq ($(wildcard $(PX4_ROOT)/src/systemcmds/auth),)  
-#MODULES		+= systemcmds/auth
-#endif
-#ifneq ($(wildcard $(PX4_ROOT)/src/modules/libtomfastmath),)  
-#MODULES	        += modules/libtomfastmath
-#MODULES         += modules/libtomcrypt
-#endif
-
-#
-# Transitional support - add commands from the NuttX export archive.
-#
-# In general, these should move to modules over time.
-#
-# Each entry here is <command>.<priority>.<stacksize>.<entrypoint> but we use a helper macro
-# to make the table a bit more readable.
-#
-define _B
-	$(strip $1).$(or $(strip $2),SCHED_PRIORITY_DEFAULT).$(or $(strip $3),CONFIG_PTHREAD_STACK_DEFAULT).$(strip $4)
-endef
-
-#                  command                 priority                   stack  entrypoint
-BUILTIN_COMMANDS := \
-	$(call _B, sercon,                 ,                          2048,  sercon_main                ) \
-	$(call _B, serdis,                 ,                          2048,  serdis_main                )
diff --git a/mk/make.inc b/mk/make.inc
deleted file mode 100644
index f4d155052e..0000000000
--- a/mk/make.inc
+++ /dev/null
@@ -1,27 +0,0 @@
-# libraries linked into every program
-LIBRARIES += AP_Module
-LIBRARIES += AP_Button
-LIBRARIES += AP_ICEngine
-LIBRARIES += AP_FlashStorage
-LIBRARIES += SRV_Channel
-LIBRARIES += AP_UAVCAN
-LIBRARIES += AP_ADC
-LIBRARIES += AP_Airspeed
-LIBRARIES += AP_Relay
-LIBRARIES += AP_ServoRelayEvents
-LIBRARIES += AP_Volz_Protocol
-LIBRARIES += AP_SBusOut
-LIBRARIES += AP_TempCalibration
-LIBRARIES += AP_Radio
-LIBRARIES += AP_Param_Helper
-LIBRARIES += AP_VisualOdom
-LIBRARIES += AP_RSSI
-LIBRARIES += AP_Proximity
-LIBRARIES += AP_Gripper
-LIBRARIES += AP_RTC
-LIBRARIES += AP_ROMFS
-LIBRARIES += AC_Sprayer
-LIBRARIES += AC_Avoidance
-LIBRARIES += AP_LandingGear
-LIBRARIES += AC_AutoTune
-LIBRARIES += AP_RobotisServo