diff --git a/Tools/ArduPPM/WorkBasket/Jeti_Duplex/Jetibox/JetiBox.h b/Tools/ArduPPM/WorkBasket/Jeti_Duplex/Jetibox/JetiBox.h
index ee39e5a2e8..d18f104ea0 100644
--- a/Tools/ArduPPM/WorkBasket/Jeti_Duplex/Jetibox/JetiBox.h
+++ b/Tools/ArduPPM/WorkBasket/Jeti_Duplex/Jetibox/JetiBox.h
@@ -24,7 +24,7 @@
 #define JetiBox_h
 
 #include <inttypes.h>
-#include "Print.h"
+#include <AP_HAL/utility/Print.h>
 
 #define jbox_key_up 0b0010
 #define jbox_key_right 0b0001
diff --git a/Tools/CPUInfo/CPUInfo.cpp b/Tools/CPUInfo/CPUInfo.cpp
index 42a36dbc45..0f19e8e9df 100644
--- a/Tools/CPUInfo/CPUInfo.cpp
+++ b/Tools/CPUInfo/CPUInfo.cpp
@@ -5,39 +5,39 @@
   Andrew Tridgell September 2011
 */
 
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
-#include <AP_HAL_SITL.h>
-#include <AP_HAL_PX4.h>
-#include <AP_HAL_Empty.h>
-#include <AP_Common.h>
-#include <AP_Scheduler.h>
-#include <AP_Baro.h>
-#include <AP_ADC.h>
-#include <AP_GPS.h>
-#include <AP_InertialSensor.h>
-#include <AP_Notify.h>
-#include <DataFlash.h>
-#include <GCS_MAVLink.h>
-#include <AP_Compass.h>
-#include <AP_Declination.h>
-#include <SITL.h>
-#include <Filter.h>
-#include <AP_Param.h>
-#include <StorageManager.h>
-#include <AP_Progmem.h>
-#include <AP_Math.h>
-#include <AP_AHRS.h>
-#include <AP_NavEKF.h>
-#include <AP_Airspeed.h>
-#include <AP_Vehicle.h>
-#include <AP_Mission.h>
-#include <AP_Terrain.h>
-#include <AP_BattMonitor.h>
-#include <AP_Rally.h>
-#include <AP_ADC_AnalogSource.h>
-#include <AP_OpticalFlow.h>
-#include <AP_RangeFinder.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
+#include <AP_HAL_SITL/AP_HAL_SITL.h>
+#include <AP_HAL_PX4/AP_HAL_PX4.h>
+#include <AP_HAL_Empty/AP_HAL_Empty.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Scheduler/AP_Scheduler.h>
+#include <AP_Baro/AP_Baro.h>
+#include <AP_ADC/AP_ADC.h>
+#include <AP_GPS/AP_GPS.h>
+#include <AP_InertialSensor/AP_InertialSensor.h>
+#include <AP_Notify/AP_Notify.h>
+#include <DataFlash/DataFlash.h>
+#include <GCS_MAVLink/GCS_MAVLink.h>
+#include <AP_Compass/AP_Compass.h>
+#include <AP_Declination/AP_Declination.h>
+#include <SITL/SITL.h>
+#include <Filter/Filter.h>
+#include <AP_Param/AP_Param.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_Progmem/AP_Progmem.h>
+#include <AP_Math/AP_Math.h>
+#include <AP_AHRS/AP_AHRS.h>
+#include <AP_NavEKF/AP_NavEKF.h>
+#include <AP_Airspeed/AP_Airspeed.h>
+#include <AP_Vehicle/AP_Vehicle.h>
+#include <AP_Mission/AP_Mission.h>
+#include <AP_Terrain/AP_Terrain.h>
+#include <AP_BattMonitor/AP_BattMonitor.h>
+#include <AP_Rally/AP_Rally.h>
+#include <AP_ADC_AnalogSource/AP_ADC_AnalogSource.h>
+#include <AP_OpticalFlow/AP_OpticalFlow.h>
+#include <AP_RangeFinder/AP_RangeFinder.h>
 
 const AP_HAL::HAL& hal = AP_HAL_BOARD_DRIVER;
 
diff --git a/Tools/Failsafe/Failsafe.pde b/Tools/Failsafe/Failsafe.pde
index 6780359662..ec91a02b5d 100644
--- a/Tools/Failsafe/Failsafe.pde
+++ b/Tools/Failsafe/Failsafe.pde
@@ -9,8 +9,8 @@ version 2.1 of the License, or (at your option) any later version.
 
 // Libraries
 #include <FastSerial.h>
-#include <AP_Common.h>
-#include <AP_Math.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Math/AP_Math.h>
 #include <Arduino_Mega_ISR_Registry.h>
 #include <APM_RC.h>         // ArduPilot Mega RC Library
 
diff --git a/Tools/FlightGear/FGShim.c b/Tools/FlightGear/FGShim.c
index 9879122cca..3e756020f7 100644
--- a/Tools/FlightGear/FGShim.c
+++ b/Tools/FlightGear/FGShim.c
@@ -59,12 +59,12 @@
 #include <unistd.h>
 
 #pragma pack(1)
-#include "mavlink_types.h"
+#include <GCS_MAVLink/include/mavlink/v1.0/mavlink_types.h>
 
 mavlink_system_t         mavlink_system;
 void                    comm_send_ch(mavlink_channel_t chan, uint8_t ch);
 #define MAVLINK_USE_CONVENIENCE_FUNCTIONS
-#include "ardupilotmega/mavlink.h"
+#include <GCS_MAVLink/include/mavlink/v1.0/ardupilotmega/mavlink.h>
 
 #define TARGET_SYSTEM           7       /* XXX what should these really be? */
 #define TARGET_COMPONENT        1
diff --git a/Tools/Hello/Hello.cpp b/Tools/Hello/Hello.cpp
index 61a8521b50..f1038cac6f 100644
--- a/Tools/Hello/Hello.cpp
+++ b/Tools/Hello/Hello.cpp
@@ -5,30 +5,30 @@
   Andrew Tridgell September 2011
 */
 
-#include <AP_Common.h>
-#include <AP_Progmem.h>
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
-#include <AP_HAL_SITL.h>
-#include <AP_HAL_PX4.h>
-#include <AP_HAL_Empty.h>
-#include <AP_Math.h>
-#include <Filter.h>
-#include <AP_InertialSensor.h>
-#include <AP_ADC.h>
-#include <GCS_MAVLink.h>
-#include <AP_Param.h>
-#include <AP_Baro.h>
-#include <AP_Compass.h>
-#include <AP_Declination.h>
-#include <SITL.h>
-#include <DataFlash.h>
-#include <AP_GPS.h>
-#include <AP_AHRS.h>
-#include <AP_Airspeed.h>
-#include <AP_Vehicle.h>
-#include <AP_ADC_AnalogSource.h>
-#include <AP_Notify.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Progmem/AP_Progmem.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
+#include <AP_HAL_SITL/AP_HAL_SITL.h>
+#include <AP_HAL_PX4/AP_HAL_PX4.h>
+#include <AP_HAL_Empty/AP_HAL_Empty.h>
+#include <AP_Math/AP_Math.h>
+#include <Filter/Filter.h>
+#include <AP_InertialSensor/AP_InertialSensor.h>
+#include <AP_ADC/AP_ADC.h>
+#include <GCS_MAVLink/GCS_MAVLink.h>
+#include <AP_Param/AP_Param.h>
+#include <AP_Baro/AP_Baro.h>
+#include <AP_Compass/AP_Compass.h>
+#include <AP_Declination/AP_Declination.h>
+#include <SITL/SITL.h>
+#include <DataFlash/DataFlash.h>
+#include <AP_GPS/AP_GPS.h>
+#include <AP_AHRS/AP_AHRS.h>
+#include <AP_Airspeed/AP_Airspeed.h>
+#include <AP_Vehicle/AP_Vehicle.h>
+#include <AP_ADC_AnalogSource/AP_ADC_AnalogSource.h>
+#include <AP_Notify/AP_Notify.h>
 
 const AP_HAL::HAL& hal = AP_HAL_BOARD_DRIVER;
 
diff --git a/Tools/Replay/DataFlashFileReader.h b/Tools/Replay/DataFlashFileReader.h
index 7f8fe81451..ef461fd832 100644
--- a/Tools/Replay/DataFlashFileReader.h
+++ b/Tools/Replay/DataFlashFileReader.h
@@ -1,7 +1,7 @@
 #ifndef REPLAY_DATAFLASHREADER_H
 #define REPLAY_DATAFLASHREADER_H
 
-#include <DataFlash.h>
+#include <DataFlash/DataFlash.h>
 
 class DataFlashFileReader
 {
diff --git a/Tools/Replay/LR_MsgHandler.cpp b/Tools/Replay/LR_MsgHandler.cpp
index af5330f215..3e37c0e908 100644
--- a/Tools/Replay/LR_MsgHandler.cpp
+++ b/Tools/Replay/LR_MsgHandler.cpp
@@ -296,7 +296,7 @@ void LR_MsgHandler_MAG::process_message(uint8_t *msg)
     update_from_msg_compass(0, msg);
 }
 
-#include <AP_AHRS.h>
+#include <AP_AHRS/AP_AHRS.h>
 #include "VehicleType.h"
 
 void LR_MsgHandler_MSG::process_message(uint8_t *msg)
diff --git a/Tools/Replay/LogReader.cpp b/Tools/Replay/LogReader.cpp
index dcdb2bf762..e7e68ac9bb 100644
--- a/Tools/Replay/LogReader.cpp
+++ b/Tools/Replay/LogReader.cpp
@@ -1,13 +1,13 @@
-#include <AP_HAL.h>
-#include <AP_Common.h>
-#include <AP_Math.h>
-#include <AP_Airspeed.h>
-#include <AP_Compass.h>
-#include <AP_GPS.h>
-#include <AP_Compass.h>
-#include <AP_Baro.h>
-#include <AP_InertialSensor.h>
-#include <DataFlash.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Math/AP_Math.h>
+#include <AP_Airspeed/AP_Airspeed.h>
+#include <AP_Compass/AP_Compass.h>
+#include <AP_GPS/AP_GPS.h>
+#include <AP_Compass/AP_Compass.h>
+#include <AP_Baro/AP_Baro.h>
+#include <AP_InertialSensor/AP_InertialSensor.h>
+#include <DataFlash/DataFlash.h>
 
 #include "LogReader.h"
 #include <stdio.h>
diff --git a/Tools/Replay/MsgHandler.h b/Tools/Replay/MsgHandler.h
index d29ce81e3f..c026fe5cbb 100644
--- a/Tools/Replay/MsgHandler.h
+++ b/Tools/Replay/MsgHandler.h
@@ -1,7 +1,7 @@
 #ifndef AP_MSGHANDLER_H
 #define AP_MSGHANDLER_H
 
-#include <DataFlash.h>
+#include <DataFlash/DataFlash.h>
 #include "VehicleType.h"
 
 #include <stdio.h>
diff --git a/Tools/Replay/Parameters.h b/Tools/Replay/Parameters.h
index e445c2defb..acd2d8188d 100644
--- a/Tools/Replay/Parameters.h
+++ b/Tools/Replay/Parameters.h
@@ -3,7 +3,7 @@
 #ifndef PARAMETERS_H
 #define PARAMETERS_H
 
-#include <AP_Common.h>
+#include <AP_Common/AP_Common.h>
 
 // Global parameter class.
 //
diff --git a/Tools/Replay/Replay.cpp b/Tools/Replay/Replay.cpp
index ac14179af0..9b112110e3 100644
--- a/Tools/Replay/Replay.cpp
+++ b/Tools/Replay/Replay.cpp
@@ -14,48 +14,48 @@
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <AP_Common.h>
-#include <AP_Progmem.h>
-#include <AP_Param.h>
-#include <StorageManager.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Progmem/AP_Progmem.h>
+#include <AP_Param/AP_Param.h>
+#include <StorageManager/StorageManager.h>
 #include <fenv.h>
-#include <AP_Math.h>
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
-#include <AP_HAL_SITL.h>
-#include <AP_HAL_Linux.h>
-#include <AP_HAL_Empty.h>
-#include <AP_ADC.h>
-#include <AP_Declination.h>
-#include <AP_ADC_AnalogSource.h>
-#include <Filter.h>
-#include <AP_Buffer.h>
-#include <AP_Airspeed.h>
-#include <AP_Vehicle.h>
-#include <AP_Notify.h>
-#include <DataFlash.h>
-#include <GCS_MAVLink.h>
-#include <AP_GPS.h>
-#include <AP_AHRS.h>
-#include <SITL.h>
-#include <AP_Compass.h>
-#include <AP_Baro.h>
-#include <AP_InertialSensor.h>
-#include <AP_InertialNav.h>
-#include <AP_NavEKF.h>
-#include <AP_Mission.h>
-#include <AP_Rally.h>
-#include <AP_BattMonitor.h>
-#include <AP_Terrain.h>
-#include <AP_OpticalFlow.h>
-#include <AP_SerialManager.h>
-#include <RC_Channel.h>
-#include <AP_RangeFinder.h>
+#include <AP_Math/AP_Math.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
+#include <AP_HAL_SITL/AP_HAL_SITL.h>
+#include <AP_HAL_Linux/AP_HAL_Linux.h>
+#include <AP_HAL_Empty/AP_HAL_Empty.h>
+#include <AP_ADC/AP_ADC.h>
+#include <AP_Declination/AP_Declination.h>
+#include <AP_ADC_AnalogSource/AP_ADC_AnalogSource.h>
+#include <Filter/Filter.h>
+#include <AP_Buffer/AP_Buffer.h>
+#include <AP_Airspeed/AP_Airspeed.h>
+#include <AP_Vehicle/AP_Vehicle.h>
+#include <AP_Notify/AP_Notify.h>
+#include <DataFlash/DataFlash.h>
+#include <GCS_MAVLink/GCS_MAVLink.h>
+#include <AP_GPS/AP_GPS.h>
+#include <AP_AHRS/AP_AHRS.h>
+#include <SITL/SITL.h>
+#include <AP_Compass/AP_Compass.h>
+#include <AP_Baro/AP_Baro.h>
+#include <AP_InertialSensor/AP_InertialSensor.h>
+#include <AP_InertialNav/AP_InertialNav.h>
+#include <AP_NavEKF/AP_NavEKF.h>
+#include <AP_Mission/AP_Mission.h>
+#include <AP_Rally/AP_Rally.h>
+#include <AP_BattMonitor/AP_BattMonitor.h>
+#include <AP_Terrain/AP_Terrain.h>
+#include <AP_OpticalFlow/AP_OpticalFlow.h>
+#include <AP_SerialManager/AP_SerialManager.h>
+#include <RC_Channel/RC_Channel.h>
+#include <AP_RangeFinder/AP_RangeFinder.h>
 #include <stdio.h>
 #include <errno.h>
 #include <signal.h>
 #include <unistd.h>
-#include <utility/getopt_cpp.h>
+#include <AP_HAL/utility/getopt_cpp.h>
 #include "Parameters.h"
 #include "VehicleType.h"
 #include "MsgHandler.h"