diff --git a/libraries/AP_Mission/AP_Mission.cpp b/libraries/AP_Mission/AP_Mission.cpp
index 3e2a5eed82..e50eb809b5 100644
--- a/libraries/AP_Mission/AP_Mission.cpp
+++ b/libraries/AP_Mission/AP_Mission.cpp
@@ -4,7 +4,7 @@
 /// @brief   Handles the MAVLINK command mission stack.  Reads and writes mission to storage.
 
 #include "AP_Mission.h"
-#include <AP_Terrain.h>
+#include <AP_Terrain/AP_Terrain.h>
 
 const AP_Param::GroupInfo AP_Mission::var_info[] PROGMEM = {
 
diff --git a/libraries/AP_Mission/AP_Mission.h b/libraries/AP_Mission/AP_Mission.h
index b8e89b9e10..22706d6b3d 100644
--- a/libraries/AP_Mission/AP_Mission.h
+++ b/libraries/AP_Mission/AP_Mission.h
@@ -15,14 +15,14 @@
 #ifndef AP_Mission_h
 #define AP_Mission_h
 
-#include <AP_HAL.h>
-#include <AP_Vehicle.h>
-#include <GCS_MAVLink.h>
-#include <AP_Math.h>
-#include <AP_Common.h>
-#include <AP_Param.h>
-#include <AP_AHRS.h>
-#include <../StorageManager/StorageManager.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_Vehicle/AP_Vehicle.h>
+#include <GCS_MAVLink/GCS_MAVLink.h>
+#include <AP_Math/AP_Math.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Param/AP_Param.h>
+#include <AP_AHRS/AP_AHRS.h>
+#include <StorageManager/StorageManager.h>
 
 // definitions
 #define AP_MISSION_EEPROM_VERSION           0x65AE  // version number stored in first four bytes of eeprom.  increment this by one when eeprom format is changed
diff --git a/libraries/AP_Mission/examples/AP_Mission_test/AP_Mission_test.cpp b/libraries/AP_Mission/examples/AP_Mission_test/AP_Mission_test.cpp
index c3434ea271..523bb19f60 100644
--- a/libraries/AP_Mission/examples/AP_Mission_test/AP_Mission_test.cpp
+++ b/libraries/AP_Mission/examples/AP_Mission_test/AP_Mission_test.cpp
@@ -3,40 +3,40 @@
  *  DIYDrones.com
  */
 
-#include <AP_Common.h>
-#include <AP_Progmem.h>
-#include <AP_Math.h>            // ArduPilot Mega Vector/Matrix math Library
-#include <AP_Curve.h>           // Curve used to linearlise throttle pwm to thrust
-#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_Empty.h>
-#include <SITL.h>
-#include <AP_Rally.h>
-#include <GCS_MAVLink.h>
-#include <AP_Notify.h>
-#include <AP_Vehicle.h>
-#include <DataFlash.h>
-#include <AP_Mission.h>
-#include <AP_NavEKF.h>
-#include <StorageManager.h>
-#include <AP_Terrain.h>
-#include <AP_GPS.h>             // ArduPilot GPS library
-#include <AP_ADC.h>             // ArduPilot Mega Analog to Digital Converter Library
-#include <AP_ADC_AnalogSource.h>
-#include <AP_Baro.h>            // ArduPilot Mega Barometer Library
-#include <Filter.h>
-#include <AP_Compass.h>         // ArduPilot Mega Magnetometer Library
-#include <AP_Declination.h>
-#include <AP_InertialSensor.h>  // ArduPilot Mega Inertial Sensor (accel & gyro) Library
-#include <AP_AHRS.h>
-#include <AP_Airspeed.h>
-#include <AP_Buffer.h>          // ArduPilot general purpose FIFO buffer
-#include <GCS_MAVLink.h>
-#include <AP_BattMonitor.h>
-#include <AP_RangeFinder.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Progmem/AP_Progmem.h>
+#include <AP_Math/AP_Math.h>            // ArduPilot Mega Vector/Matrix math Library
+#include <AP_Curve/AP_Curve.h>           // Curve used to linearlise throttle pwm to thrust
+#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_Empty/AP_HAL_Empty.h>
+#include <SITL/SITL.h>
+#include <AP_Rally/AP_Rally.h>
+#include <GCS_MAVLink/GCS_MAVLink.h>
+#include <AP_Notify/AP_Notify.h>
+#include <AP_Vehicle/AP_Vehicle.h>
+#include <DataFlash/DataFlash.h>
+#include <AP_Mission/AP_Mission.h>
+#include <AP_NavEKF/AP_NavEKF.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_Terrain/AP_Terrain.h>
+#include <AP_GPS/AP_GPS.h>             // ArduPilot GPS library
+#include <AP_ADC/AP_ADC.h>             // ArduPilot Mega Analog to Digital Converter Library
+#include <AP_ADC_AnalogSource/AP_ADC_AnalogSource.h>
+#include <AP_Baro/AP_Baro.h>            // ArduPilot Mega Barometer Library
+#include <Filter/Filter.h>
+#include <AP_Compass/AP_Compass.h>         // ArduPilot Mega Magnetometer Library
+#include <AP_Declination/AP_Declination.h>
+#include <AP_InertialSensor/AP_InertialSensor.h>  // ArduPilot Mega Inertial Sensor (accel & gyro) Library
+#include <AP_AHRS/AP_AHRS.h>
+#include <AP_Airspeed/AP_Airspeed.h>
+#include <AP_Buffer/AP_Buffer.h>          // ArduPilot general purpose FIFO buffer
+#include <GCS_MAVLink/GCS_MAVLink.h>
+#include <AP_BattMonitor/AP_BattMonitor.h>
+#include <AP_RangeFinder/AP_RangeFinder.h>
 
 const AP_HAL::HAL& hal = AP_HAL_BOARD_DRIVER;