diff --git a/libraries/AP_GPS/AP_GPS.cpp b/libraries/AP_GPS/AP_GPS.cpp
index 25174bda81..cbb68a5898 100644
--- a/libraries/AP_GPS/AP_GPS.cpp
+++ b/libraries/AP_GPS/AP_GPS.cpp
@@ -14,11 +14,11 @@
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <AP_Common.h>
-#include <AP_Math.h>
-#include <AP_HAL.h>
-#include <AP_Notify.h>
-#include <AP_GPS.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Math/AP_Math.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_Notify/AP_Notify.h>
+#include "AP_GPS.h"
 
 extern const AP_HAL::HAL& hal;
 
diff --git a/libraries/AP_GPS/AP_GPS.h b/libraries/AP_GPS/AP_GPS.h
index 6968d42dfb..56c28c9595 100644
--- a/libraries/AP_GPS/AP_GPS.h
+++ b/libraries/AP_GPS/AP_GPS.h
@@ -17,14 +17,14 @@
 #ifndef __AP_GPS_H__
 #define __AP_GPS_H__
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #include <inttypes.h>
-#include <AP_Progmem.h>
-#include <AP_Common.h>
-#include <AP_Param.h>
-#include <AP_Math.h>
-#include <GCS_MAVLink.h>
-#include <AP_Vehicle.h>
+#include <AP_Progmem/AP_Progmem.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Param/AP_Param.h>
+#include <AP_Math/AP_Math.h>
+#include <GCS_MAVLink/GCS_MAVLink.h>
+#include <AP_Vehicle/AP_Vehicle.h>
 #include "GPS_detect_state.h"
 #include "../AP_SerialManager/AP_SerialManager.h"
 
@@ -416,13 +416,13 @@ private:
 
 #define GPS_BAUD_TIME_MS 1200
 
-#include <GPS_Backend.h>
-#include <AP_GPS_UBLOX.h>
-#include <AP_GPS_MTK.h>
-#include <AP_GPS_MTK19.h>
-#include <AP_GPS_NMEA.h>
-#include <AP_GPS_SIRF.h>
-#include <AP_GPS_SBP.h>
-#include <AP_GPS_PX4.h>
+#include "GPS_Backend.h"
+#include "AP_GPS_UBLOX.h"
+#include "AP_GPS_MTK.h"
+#include "AP_GPS_MTK19.h"
+#include "AP_GPS_NMEA.h"
+#include "AP_GPS_SIRF.h"
+#include "AP_GPS_SBP.h"
+#include "AP_GPS_PX4.h"
 
 #endif // __AP_GPS_H__
diff --git a/libraries/AP_GPS/AP_GPS_MTK.cpp b/libraries/AP_GPS/AP_GPS_MTK.cpp
index 0a0b9aabcf..eb90bed748 100644
--- a/libraries/AP_GPS/AP_GPS_MTK.cpp
+++ b/libraries/AP_GPS/AP_GPS_MTK.cpp
@@ -21,7 +21,7 @@
 //	GPS configuration : Custom protocol per "DIYDrones Custom Binary Sentence Specification V1.1"
 //
 
-#include <AP_GPS.h>
+#include "AP_GPS.h"
 #include "AP_GPS_MTK.h"
 
 // initialisation blobs to send to the GPS to try to get it into the
diff --git a/libraries/AP_GPS/AP_GPS_MTK.h b/libraries/AP_GPS/AP_GPS_MTK.h
index 504a93fb58..822f4df92a 100644
--- a/libraries/AP_GPS/AP_GPS_MTK.h
+++ b/libraries/AP_GPS/AP_GPS_MTK.h
@@ -25,7 +25,7 @@
 #ifndef __AP_GPS_MTK_H__
 #define __AP_GPS_MTK_H__
 
-#include <AP_GPS.h>
+#include "AP_GPS.h"
 #include "AP_GPS_MTK_Common.h"
 
 class AP_GPS_MTK : public AP_GPS_Backend {
diff --git a/libraries/AP_GPS/AP_GPS_MTK19.h b/libraries/AP_GPS/AP_GPS_MTK19.h
index c1323fb44d..210b9d5d96 100644
--- a/libraries/AP_GPS/AP_GPS_MTK19.h
+++ b/libraries/AP_GPS/AP_GPS_MTK19.h
@@ -23,7 +23,7 @@
 #ifndef AP_GPS_MTK19_h
 #define AP_GPS_MTK19_h
 
-#include <AP_GPS.h>
+#include "AP_GPS.h"
 #include "AP_GPS_MTK_Common.h"
 
 #define MTK_GPS_REVISION_V16  16
diff --git a/libraries/AP_GPS/AP_GPS_NMEA.cpp b/libraries/AP_GPS/AP_GPS_NMEA.cpp
index c563cd2e54..636497c073 100644
--- a/libraries/AP_GPS/AP_GPS_NMEA.cpp
+++ b/libraries/AP_GPS/AP_GPS_NMEA.cpp
@@ -29,9 +29,9 @@
 /// TinyGPS parser by Mikal Hart.
 ///
 
-#include <AP_Common.h>
+#include <AP_Common/AP_Common.h>
 
-#include <AP_Progmem.h>
+#include <AP_Progmem/AP_Progmem.h>
 #include <ctype.h>
 #include <stdint.h>
 #include <stdlib.h>
diff --git a/libraries/AP_GPS/AP_GPS_NMEA.h b/libraries/AP_GPS/AP_GPS_NMEA.h
index 1049b0ec1a..4143b3a627 100644
--- a/libraries/AP_GPS/AP_GPS_NMEA.h
+++ b/libraries/AP_GPS/AP_GPS_NMEA.h
@@ -47,7 +47,7 @@
 #ifndef __AP_GPS_NMEA_H__
 #define __AP_GPS_NMEA_H__
 
-#include <AP_GPS.h>
+#include "AP_GPS.h"
 
 /// NMEA parser
 ///
diff --git a/libraries/AP_GPS/AP_GPS_PX4.cpp b/libraries/AP_GPS/AP_GPS_PX4.cpp
index e59fd82a28..21c9d490dc 100644
--- a/libraries/AP_GPS/AP_GPS_PX4.cpp
+++ b/libraries/AP_GPS/AP_GPS_PX4.cpp
@@ -22,7 +22,7 @@
 //
 //  Code by Holger Steinhaus
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #if CONFIG_HAL_BOARD == HAL_BOARD_PX4
 #include "AP_GPS_PX4.h"
 
diff --git a/libraries/AP_GPS/AP_GPS_PX4.h b/libraries/AP_GPS/AP_GPS_PX4.h
index 837fc991cc..e59e7cb290 100644
--- a/libraries/AP_GPS/AP_GPS_PX4.h
+++ b/libraries/AP_GPS/AP_GPS_PX4.h
@@ -21,8 +21,8 @@
 #ifndef __AP_GPS_PX4_H__
 #define __AP_GPS_PX4_H__
 
-#include <AP_HAL.h>
-#include <AP_GPS.h>
+#include <AP_HAL/AP_HAL.h>
+#include "AP_GPS.h"
 #if CONFIG_HAL_BOARD == HAL_BOARD_PX4
 #include <modules/uORB/topics/vehicle_gps_position.h>
 
diff --git a/libraries/AP_GPS/AP_GPS_SBP.cpp b/libraries/AP_GPS/AP_GPS_SBP.cpp
index f151128c56..11b92fd6a6 100644
--- a/libraries/AP_GPS/AP_GPS_SBP.cpp
+++ b/libraries/AP_GPS/AP_GPS_SBP.cpp
@@ -21,9 +21,9 @@
 //  Swift Binary Protocol format: http://docs.swift-nav.com/
 //
 
-#include <AP_GPS.h>
+#include "AP_GPS.h"
 #include "AP_GPS_SBP.h"
-#include <DataFlash.h>
+#include <DataFlash/DataFlash.h>
 
 #if GPS_RTK_AVAILABLE
 
diff --git a/libraries/AP_GPS/AP_GPS_SBP.h b/libraries/AP_GPS/AP_GPS_SBP.h
index d2d445bcc7..58148af615 100644
--- a/libraries/AP_GPS/AP_GPS_SBP.h
+++ b/libraries/AP_GPS/AP_GPS_SBP.h
@@ -24,7 +24,7 @@
 #ifndef __AP_GPS_SBP_H__
 #define __AP_GPS_SBP_H__
 
-#include <AP_GPS.h>
+#include "AP_GPS.h"
 
 class AP_GPS_SBP : public AP_GPS_Backend
 {
diff --git a/libraries/AP_GPS/AP_GPS_SIRF.h b/libraries/AP_GPS/AP_GPS_SIRF.h
index 15d1ece9bf..7ee9f0aa60 100644
--- a/libraries/AP_GPS/AP_GPS_SIRF.h
+++ b/libraries/AP_GPS/AP_GPS_SIRF.h
@@ -21,9 +21,9 @@
 #ifndef __AP_GPS_SIRF_H__
 #define __AP_GPS_SIRF_H__
 
-#include <AP_HAL.h>
-#include <AP_Common.h>
-#include <AP_GPS.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_Common/AP_Common.h>
+#include "AP_GPS.h"
 
 #define SIRF_SET_BINARY "$PSRF100,0,38400,8,1,0*3C\r\n"
 
diff --git a/libraries/AP_GPS/AP_GPS_UBLOX.cpp b/libraries/AP_GPS/AP_GPS_UBLOX.cpp
index c79014c640..a4a5adbe9c 100644
--- a/libraries/AP_GPS/AP_GPS_UBLOX.cpp
+++ b/libraries/AP_GPS/AP_GPS_UBLOX.cpp
@@ -19,9 +19,9 @@
 //	Origin code by Michael Smith, Jordi Munoz and Jose Julio, DIYDrones.com
 //  Substantially rewitten for new GPS driver structure by Andrew Tridgell
 //
-#include <AP_GPS.h>
+#include "AP_GPS.h"
 #include "AP_GPS_UBLOX.h"
-#include <DataFlash.h>
+#include <DataFlash/DataFlash.h>
 
 #if CONFIG_HAL_BOARD_SUBTYPE == HAL_BOARD_SUBTYPE_LINUX_NAVIO
     #define UBLOX_VERSION_AUTODETECTION 1
diff --git a/libraries/AP_GPS/AP_GPS_UBLOX.h b/libraries/AP_GPS/AP_GPS_UBLOX.h
index 7227b6ceee..96b2d3b297 100644
--- a/libraries/AP_GPS/AP_GPS_UBLOX.h
+++ b/libraries/AP_GPS/AP_GPS_UBLOX.h
@@ -23,8 +23,8 @@
 #ifndef __AP_GPS_UBLOX_H__
 #define __AP_GPS_UBLOX_H__
 
-#include <AP_HAL.h>
-#include <AP_GPS.h>
+#include <AP_HAL/AP_HAL.h>
+#include "AP_GPS.h"
 
 /*
  *  try to put a UBlox into binary mode. This is in two parts. 
diff --git a/libraries/AP_GPS/GPS_Backend.cpp b/libraries/AP_GPS/GPS_Backend.cpp
index 0d8caae9e1..622b045a2e 100644
--- a/libraries/AP_GPS/GPS_Backend.cpp
+++ b/libraries/AP_GPS/GPS_Backend.cpp
@@ -14,7 +14,7 @@
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <AP_GPS.h>
+#include "AP_GPS.h"
 
 extern const AP_HAL::HAL& hal;
 
diff --git a/libraries/AP_GPS/GPS_Backend.h b/libraries/AP_GPS/GPS_Backend.h
index b88bbdb67e..8bbf9b016d 100644
--- a/libraries/AP_GPS/GPS_Backend.h
+++ b/libraries/AP_GPS/GPS_Backend.h
@@ -20,8 +20,8 @@
 #ifndef __AP_GPS_BACKEND_H__
 #define __AP_GPS_BACKEND_H__
 
-#include <GCS_MAVLink.h>
-#include <AP_GPS.h>
+#include <GCS_MAVLink/GCS_MAVLink.h>
+#include "AP_GPS.h"
 
 class AP_GPS_Backend
 {
diff --git a/libraries/AP_GPS/examples/GPS_AUTO_test/GPS_AUTO_test.cpp b/libraries/AP_GPS/examples/GPS_AUTO_test/GPS_AUTO_test.cpp
index 4231e34f63..4361a8e491 100644
--- a/libraries/AP_GPS/examples/GPS_AUTO_test/GPS_AUTO_test.cpp
+++ b/libraries/AP_GPS/examples/GPS_AUTO_test/GPS_AUTO_test.cpp
@@ -5,40 +5,40 @@
 
 #include <stdlib.h>
 
-#include <AP_Common.h>
-#include <AP_Progmem.h>
-#include <AP_Param.h>
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
-#include <AP_HAL_SITL.h>
-#include <AP_HAL_PX4.h>
-#include <AP_HAL_Linux.h>
-#include <AP_HAL_Empty.h>
-#include <AP_GPS.h>
-#include <DataFlash.h>
-#include <AP_InertialSensor.h>
-#include <AP_ADC.h>
-#include <GCS_MAVLink.h>
-#include <AP_Baro.h>
-#include <Filter.h>
-#include <AP_AHRS.h>
-#include <AP_Compass.h>
-#include <AP_Declination.h>
-#include <AP_Airspeed.h>
-#include <AP_Vehicle.h>
-#include <AP_ADC_AnalogSource.h>
-#include <AP_Mission.h>
-#include <StorageManager.h>
-#include <AP_Terrain.h>
-#include <AP_Math.h>
-#include <AP_Notify.h>
-#include <AP_BoardLED.h>
-#include <AP_NavEKF.h>
-#include <AP_Rally.h>
-#include <AP_Scheduler.h>
-#include <AP_BattMonitor.h>
-#include <AP_SerialManager.h>
-#include <AP_RangeFinder.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Progmem/AP_Progmem.h>
+#include <AP_Param/AP_Param.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_Linux/AP_HAL_Linux.h>
+#include <AP_HAL_Empty/AP_HAL_Empty.h>
+#include <AP_GPS/AP_GPS.h>
+#include <DataFlash/DataFlash.h>
+#include <AP_InertialSensor/AP_InertialSensor.h>
+#include <AP_ADC/AP_ADC.h>
+#include <GCS_MAVLink/GCS_MAVLink.h>
+#include <AP_Baro/AP_Baro.h>
+#include <Filter/Filter.h>
+#include <AP_AHRS/AP_AHRS.h>
+#include <AP_Compass/AP_Compass.h>
+#include <AP_Declination/AP_Declination.h>
+#include <AP_Airspeed/AP_Airspeed.h>
+#include <AP_Vehicle/AP_Vehicle.h>
+#include <AP_ADC_AnalogSource/AP_ADC_AnalogSource.h>
+#include <AP_Mission/AP_Mission.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_Terrain/AP_Terrain.h>
+#include <AP_Math/AP_Math.h>
+#include <AP_Notify/AP_Notify.h>
+#include <AP_Notify/AP_BoardLED.h>
+#include <AP_NavEKF/AP_NavEKF.h>
+#include <AP_Rally/AP_Rally.h>
+#include <AP_Scheduler/AP_Scheduler.h>
+#include <AP_BattMonitor/AP_BattMonitor.h>
+#include <AP_SerialManager/AP_SerialManager.h>
+#include <AP_RangeFinder/AP_RangeFinder.h>
 
 const AP_HAL::HAL& hal = AP_HAL_BOARD_DRIVER;
 
diff --git a/libraries/AP_GPS/examples/GPS_UBLOX_passthrough/GPS_UBLOX_passthrough.cpp b/libraries/AP_GPS/examples/GPS_UBLOX_passthrough/GPS_UBLOX_passthrough.cpp
index 361b91ab23..49748c9b07 100644
--- a/libraries/AP_GPS/examples/GPS_UBLOX_passthrough/GPS_UBLOX_passthrough.cpp
+++ b/libraries/AP_GPS/examples/GPS_UBLOX_passthrough/GPS_UBLOX_passthrough.cpp
@@ -7,37 +7,37 @@
  */
 
 #include <stdlib.h>
-#include <AP_Common.h>
-#include <AP_Progmem.h>
-#include <AP_Param.h>
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
-#include <AP_HAL_Empty.h>
-#include <AP_HAL_PX4.h>
-#include <AP_HAL_Linux.h>
-#include <AP_GPS.h>
-#include <DataFlash.h>
-#include <AP_InertialSensor.h>
-#include <AP_ADC.h>
-#include <GCS_MAVLink.h>
-#include <AP_Baro.h>
-#include <Filter.h>
-#include <AP_AHRS.h>
-#include <AP_Compass.h>
-#include <AP_Declination.h>
-#include <AP_Airspeed.h>
-#include <AP_Vehicle.h>
-#include <AP_ADC_AnalogSource.h>
-#include <AP_Mission.h>
-#include <StorageManager.h>
-#include <AP_Terrain.h>
-#include <AP_Math.h>
-#include <AP_Notify.h>
-#include <AP_NavEKF.h>
-#include <AP_Rally.h>
-#include <AP_Scheduler.h>
-#include <AP_BattMonitor.h>
-#include <AP_RangeFinder.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Progmem/AP_Progmem.h>
+#include <AP_Param/AP_Param.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
+#include <AP_HAL_Empty/AP_HAL_Empty.h>
+#include <AP_HAL_PX4/AP_HAL_PX4.h>
+#include <AP_HAL_Linux/AP_HAL_Linux.h>
+#include <AP_GPS/AP_GPS.h>
+#include <DataFlash/DataFlash.h>
+#include <AP_InertialSensor/AP_InertialSensor.h>
+#include <AP_ADC/AP_ADC.h>
+#include <GCS_MAVLink/GCS_MAVLink.h>
+#include <AP_Baro/AP_Baro.h>
+#include <Filter/Filter.h>
+#include <AP_AHRS/AP_AHRS.h>
+#include <AP_Compass/AP_Compass.h>
+#include <AP_Declination/AP_Declination.h>
+#include <AP_Airspeed/AP_Airspeed.h>
+#include <AP_Vehicle/AP_Vehicle.h>
+#include <AP_ADC_AnalogSource/AP_ADC_AnalogSource.h>
+#include <AP_Mission/AP_Mission.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_Terrain/AP_Terrain.h>
+#include <AP_Math/AP_Math.h>
+#include <AP_Notify/AP_Notify.h>
+#include <AP_NavEKF/AP_NavEKF.h>
+#include <AP_Rally/AP_Rally.h>
+#include <AP_Scheduler/AP_Scheduler.h>
+#include <AP_BattMonitor/AP_BattMonitor.h>
+#include <AP_RangeFinder/AP_RangeFinder.h>
 
 const AP_HAL::HAL& hal = AP_HAL_BOARD_DRIVER;