diff --git a/libraries/GCS_MAVLink/GCS.h b/libraries/GCS_MAVLink/GCS.h
index 81f222a184..423e5f2793 100644
--- a/libraries/GCS_MAVLink/GCS.h
+++ b/libraries/GCS_MAVLink/GCS.h
@@ -7,14 +7,14 @@
 #ifndef __GCS_H
 #define __GCS_H
 
-#include <AP_HAL.h>
-#include <AP_Common.h>
-#include <GCS_MAVLink.h>
-#include <DataFlash.h>
-#include <AP_Mission.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_Common/AP_Common.h>
+#include "GCS_MAVLink.h"
+#include <DataFlash/DataFlash.h>
+#include <AP_Mission/AP_Mission.h>
 #include "../AP_BattMonitor/AP_BattMonitor.h"
 #include <stdint.h>
-#include <MAVLink_routing.h>
+#include "MAVLink_routing.h"
 #include "../AP_SerialManager/AP_SerialManager.h"
 #include "../AP_Mount/AP_Mount.h"
 
diff --git a/libraries/GCS_MAVLink/GCS_Common.cpp b/libraries/GCS_MAVLink/GCS_Common.cpp
index 47b25b9010..837ca5ee2e 100644
--- a/libraries/GCS_MAVLink/GCS_Common.cpp
+++ b/libraries/GCS_MAVLink/GCS_Common.cpp
@@ -17,10 +17,10 @@
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <GCS.h>
-#include <AP_AHRS.h>
-#include <AP_HAL.h>
-#include <AP_Vehicle.h>
+#include "GCS.h"
+#include <AP_AHRS/AP_AHRS.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_Vehicle/AP_Vehicle.h>
 
 extern const AP_HAL::HAL& hal;
 
diff --git a/libraries/GCS_MAVLink/GCS_Logs.cpp b/libraries/GCS_MAVLink/GCS_Logs.cpp
index 7fa3c1caa3..da93f93e70 100644
--- a/libraries/GCS_MAVLink/GCS_Logs.cpp
+++ b/libraries/GCS_MAVLink/GCS_Logs.cpp
@@ -19,9 +19,9 @@
  */
 
 
-#include <AP_HAL.h>
-#include <GCS.h>
-#include <DataFlash.h>
+#include <AP_HAL/AP_HAL.h>
+#include "GCS.h"
+#include <DataFlash/DataFlash.h>
 
 extern const AP_HAL::HAL& hal;
 
diff --git a/libraries/GCS_MAVLink/GCS_MAVLink.cpp b/libraries/GCS_MAVLink/GCS_MAVLink.cpp
index 69ed2f1af7..e43e22f039 100644
--- a/libraries/GCS_MAVLink/GCS_MAVLink.cpp
+++ b/libraries/GCS_MAVLink/GCS_MAVLink.cpp
@@ -21,11 +21,11 @@ This provides some support code and variables for MAVLink enabled sketches
 
 */
 
-#include <AP_HAL.h>
-#include <AP_Common.h>
-#include <GCS_MAVLink.h>
-#include <GCS.h>
-#include <AP_GPS.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_Common/AP_Common.h>
+#include "GCS_MAVLink.h"
+#include "GCS.h"
+#include <AP_GPS/AP_GPS.h>
 
 #ifdef MAVLINK_SEPARATE_HELPERS
 #include "include/mavlink/v1.0/mavlink_helpers.h"
diff --git a/libraries/GCS_MAVLink/GCS_MAVLink.h b/libraries/GCS_MAVLink/GCS_MAVLink.h
index 1324a3c33d..c659f72260 100644
--- a/libraries/GCS_MAVLink/GCS_MAVLink.h
+++ b/libraries/GCS_MAVLink/GCS_MAVLink.h
@@ -6,9 +6,9 @@
 #ifndef GCS_MAVLink_h
 #define GCS_MAVLink_h
 
-#include <AP_HAL.h>
-#include <AP_Param.h>
-#include <AP_Math.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_Param/AP_Param.h>
+#include <AP_Math/AP_Math.h>
 
 // we have separate helpers disabled to make it possible
 // to select MAVLink 1.0 in the arduino GUI build
diff --git a/libraries/GCS_MAVLink/GCS_serial_control.cpp b/libraries/GCS_MAVLink/GCS_serial_control.cpp
index 570ec31eb1..83bde14fc6 100644
--- a/libraries/GCS_MAVLink/GCS_serial_control.cpp
+++ b/libraries/GCS_MAVLink/GCS_serial_control.cpp
@@ -19,9 +19,9 @@
  */
 
 
-#include <AP_HAL.h>
-#include <GCS.h>
-#include <DataFlash.h>
+#include <AP_HAL/AP_HAL.h>
+#include "GCS.h"
+#include <DataFlash/DataFlash.h>
 
 extern const AP_HAL::HAL& hal;
 
diff --git a/libraries/GCS_MAVLink/MAVLink_routing.cpp b/libraries/GCS_MAVLink/MAVLink_routing.cpp
index 3f7ac03e70..12ade32671 100644
--- a/libraries/GCS_MAVLink/MAVLink_routing.cpp
+++ b/libraries/GCS_MAVLink/MAVLink_routing.cpp
@@ -19,10 +19,10 @@
 /// @brief	handle routing of MAVLink packets by sysid/componentid
 
 #include <stdio.h>
-#include <AP_HAL.h>
-#include <AP_Common.h>
-#include <GCS.h>
-#include <MAVLink_routing.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_Common/AP_Common.h>
+#include "GCS.h"
+#include "MAVLink_routing.h"
 
 extern const AP_HAL::HAL& hal;
 
diff --git a/libraries/GCS_MAVLink/MAVLink_routing.h b/libraries/GCS_MAVLink/MAVLink_routing.h
index 3db08b60fc..f9dcfce38c 100644
--- a/libraries/GCS_MAVLink/MAVLink_routing.h
+++ b/libraries/GCS_MAVLink/MAVLink_routing.h
@@ -6,9 +6,9 @@
 #ifndef __MAVLINK_ROUTING_H
 #define __MAVLINK_ROUTING_H
 
-#include <AP_HAL.h>
-#include <AP_Common.h>
-#include <GCS_MAVLink.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_Common/AP_Common.h>
+#include "GCS_MAVLink.h"
 
 // 20 routes should be enough for now. This may need to increase as
 // we make more extensive use of MAVLink forwarding
diff --git a/libraries/GCS_MAVLink/examples/routing/routing.cpp b/libraries/GCS_MAVLink/examples/routing/routing.cpp
index d7cc04c24b..7e74c53333 100644
--- a/libraries/GCS_MAVLink/examples/routing/routing.cpp
+++ b/libraries/GCS_MAVLink/examples/routing/routing.cpp
@@ -5,43 +5,43 @@
 //
 
 #include <stdarg.h>
-#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_Linux.h>
-#include <AP_HAL_FLYMAPLE.h>
-#include <AP_HAL_PX4.h>
-#include <AP_HAL_Empty.h>
-#include <AP_Math.h>
-#include <AP_Param.h>
-#include <StorageManager.h>
-#include <AP_ADC.h>
-#include <AP_InertialSensor.h>
-#include <AP_Notify.h>
-#include <AP_GPS.h>
-#include <AP_Baro.h>
-#include <Filter.h>
-#include <DataFlash.h>
-#include <GCS_MAVLink.h>
-#include <GCS.h>
-#include <AP_Mission.h>
-#include <StorageManager.h>
-#include <AP_Terrain.h>
-#include <AP_AHRS.h>
-#include <AP_Airspeed.h>
-#include <AP_Vehicle.h>
-#include <AP_ADC_AnalogSource.h>
-#include <AP_Compass.h>
-#include <AP_Declination.h>
-#include <AP_NavEKF.h>
-#include <AP_HAL_Linux.h>
-#include <AP_Rally.h>
-#include <AP_Scheduler.h>
-#include <AP_BattMonitor.h>
-#include <SITL.h>
-#include <AP_RangeFinder.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_Linux/AP_HAL_Linux.h>
+#include <AP_HAL_FLYMAPLE/AP_HAL_FLYMAPLE.h>
+#include <AP_HAL_PX4/AP_HAL_PX4.h>
+#include <AP_HAL_Empty/AP_HAL_Empty.h>
+#include <AP_Math/AP_Math.h>
+#include <AP_Param/AP_Param.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_ADC/AP_ADC.h>
+#include <AP_InertialSensor/AP_InertialSensor.h>
+#include <AP_Notify/AP_Notify.h>
+#include <AP_GPS/AP_GPS.h>
+#include <AP_Baro/AP_Baro.h>
+#include <Filter/Filter.h>
+#include <DataFlash/DataFlash.h>
+#include <GCS_MAVLink/GCS_MAVLink.h>
+#include <GCS_MAVLink/GCS.h>
+#include <AP_Mission/AP_Mission.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_Terrain/AP_Terrain.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_Compass/AP_Compass.h>
+#include <AP_Declination/AP_Declination.h>
+#include <AP_NavEKF/AP_NavEKF.h>
+#include <AP_HAL_Linux/AP_HAL_Linux.h>
+#include <AP_Rally/AP_Rally.h>
+#include <AP_Scheduler/AP_Scheduler.h>
+#include <AP_BattMonitor/AP_BattMonitor.h>
+#include <SITL/SITL.h>
+#include <AP_RangeFinder/AP_RangeFinder.h>
 
 const AP_HAL::HAL& hal = AP_HAL_BOARD_DRIVER;
 
diff --git a/libraries/GCS_MAVLink/include/mavlink/v1.0/mavlink_protobuf_manager.hpp b/libraries/GCS_MAVLink/include/mavlink/v1.0/mavlink_protobuf_manager.hpp
index fd3ddd026f..b53d6f6d69 100644
--- a/libraries/GCS_MAVLink/include/mavlink/v1.0/mavlink_protobuf_manager.hpp
+++ b/libraries/GCS_MAVLink/include/mavlink/v1.0/mavlink_protobuf_manager.hpp
@@ -6,9 +6,9 @@
 #include <iostream>
 #include <tr1/memory>
 
-#include <checksum.h>
-#include <common/mavlink.h>
-#include <mavlink_types.h>
+#include "checksum.h"
+#include "common/mavlink.h"
+#include "mavlink_types.h"
 #include <pixhawk/pixhawk.pb.h>
 
 namespace mavlink