diff --git a/libraries/AP_HAL_AVR/AP_HAL_AVR.h b/libraries/AP_HAL_AVR/AP_HAL_AVR.h
index 16579428c7..c288234949 100644
--- a/libraries/AP_HAL_AVR/AP_HAL_AVR.h
+++ b/libraries/AP_HAL_AVR/AP_HAL_AVR.h
@@ -2,7 +2,7 @@
 #ifndef __AP_HAL_AVR_H__
 #define __AP_HAL_AVR_H__
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM1 || CONFIG_HAL_BOARD == HAL_BOARD_APM2
 /**
diff --git a/libraries/AP_HAL_AVR/AnalogIn.h b/libraries/AP_HAL_AVR/AnalogIn.h
index 5e0d0a2d0b..028128d26e 100644
--- a/libraries/AP_HAL_AVR/AnalogIn.h
+++ b/libraries/AP_HAL_AVR/AnalogIn.h
@@ -2,7 +2,7 @@
 #ifndef __AP_HAL_AVR_ANALOG_IN_H__
 #define __AP_HAL_AVR_ANALOG_IN_H__
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #include "AP_HAL_AVR_Namespace.h"
 
 #define AVR_INPUT_MAX_CHANNELS 12
diff --git a/libraries/AP_HAL_AVR/AnalogIn_ADC.cpp b/libraries/AP_HAL_AVR/AnalogIn_ADC.cpp
index ecc90c329d..054a00c3c7 100644
--- a/libraries/AP_HAL_AVR/AnalogIn_ADC.cpp
+++ b/libraries/AP_HAL_AVR/AnalogIn_ADC.cpp
@@ -1,6 +1,6 @@
 /// -*- tab-width: 4; Mode: C++; c-basic-offset: 4; indent-tabs-mode: nil -*-
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #if (CONFIG_HAL_BOARD == HAL_BOARD_APM1 || CONFIG_HAL_BOARD == HAL_BOARD_APM2)
 
 #include <avr/io.h>
diff --git a/libraries/AP_HAL_AVR/AnalogIn_Common.cpp b/libraries/AP_HAL_AVR/AnalogIn_Common.cpp
index 99248363a5..a0285d4ac0 100644
--- a/libraries/AP_HAL_AVR/AnalogIn_Common.cpp
+++ b/libraries/AP_HAL_AVR/AnalogIn_Common.cpp
@@ -1,12 +1,12 @@
 /// -*- tab-width: 4; Mode: C++; c-basic-offset: 4; indent-tabs-mode: nil -*-
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #if (CONFIG_HAL_BOARD == HAL_BOARD_APM1 || CONFIG_HAL_BOARD == HAL_BOARD_APM2)
 
 #include <avr/io.h>
 #include <avr/interrupt.h>
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #include "AnalogIn.h"
 using namespace AP_HAL_AVR;
 
diff --git a/libraries/AP_HAL_AVR/GPIO.cpp b/libraries/AP_HAL_AVR/GPIO.cpp
index 393950d5fa..45684b30af 100644
--- a/libraries/AP_HAL_AVR/GPIO.cpp
+++ b/libraries/AP_HAL_AVR/GPIO.cpp
@@ -1,4 +1,4 @@
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #if (CONFIG_HAL_BOARD == HAL_BOARD_APM1 || CONFIG_HAL_BOARD == HAL_BOARD_APM2)
 
 #include <avr/interrupt.h>
diff --git a/libraries/AP_HAL_AVR/GPIO.h b/libraries/AP_HAL_AVR/GPIO.h
index 9e8a5628b3..729876ad96 100644
--- a/libraries/AP_HAL_AVR/GPIO.h
+++ b/libraries/AP_HAL_AVR/GPIO.h
@@ -2,7 +2,7 @@
 #ifndef __AP_HAL_AVR_GPIO_H__
 #define __AP_HAL_AVR_GPIO_H__
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #include "AP_HAL_AVR_Namespace.h"
 
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM1
diff --git a/libraries/AP_HAL_AVR/HAL_AVR_APM1_Class.cpp b/libraries/AP_HAL_AVR/HAL_AVR_APM1_Class.cpp
index f4ff3a7b34..973ea85265 100644
--- a/libraries/AP_HAL_AVR/HAL_AVR_APM1_Class.cpp
+++ b/libraries/AP_HAL_AVR/HAL_AVR_APM1_Class.cpp
@@ -1,12 +1,12 @@
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 
 /* To save linker space, we need to make sure the HAL_AVR_APM1 class
  * is built iff we are building for HAL_BOARD_APM1. These defines must
  * wrap the whole HAL_AVR_APM1 class declaration and definition. */
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM1
 
-#include <AP_HAL_AVR.h>
+#include "AP_HAL_AVR.h"
 #include "AP_HAL_AVR_private.h"
 #include "HAL_AVR_APM1_Class.h"
 
diff --git a/libraries/AP_HAL_AVR/HAL_AVR_APM1_Class.h b/libraries/AP_HAL_AVR/HAL_AVR_APM1_Class.h
index f63911ce41..1c367f3e43 100644
--- a/libraries/AP_HAL_AVR/HAL_AVR_APM1_Class.h
+++ b/libraries/AP_HAL_AVR/HAL_AVR_APM1_Class.h
@@ -2,14 +2,14 @@
 #ifndef __AP_HAL_AVR_APM1_HAL_AVR_H__
 #define __AP_HAL_AVR_APM1_HAL_AVR_H__
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 
 /* To save linker space, we need to make sure the HAL_AVR_APM1 class
  * is built iff we are building for HAL_BOARD_APM1. These defines must
  * wrap the whole HAL_AVR_APM1 class declaration and definition. */
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM1
 
-#include <AP_HAL_AVR.h>
+#include "AP_HAL_AVR.h"
 #include "AP_HAL_AVR_Namespace.h"
 
 /**
diff --git a/libraries/AP_HAL_AVR/HAL_AVR_APM2_Class.cpp b/libraries/AP_HAL_AVR/HAL_AVR_APM2_Class.cpp
index f3028d3229..6a83ed917f 100644
--- a/libraries/AP_HAL_AVR/HAL_AVR_APM2_Class.cpp
+++ b/libraries/AP_HAL_AVR/HAL_AVR_APM2_Class.cpp
@@ -1,12 +1,12 @@
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 
 /* To save linker space, we need to make sure the HAL_AVR_APM2 class
  * is built iff we are building for HAL_BOARD_APM2. These defines must
  * wrap the whole HAL_AVR_APM2 class declaration and definition. */
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM2
 
-#include <AP_HAL_AVR.h>
+#include "AP_HAL_AVR.h"
 #include "AP_HAL_AVR_private.h"
 #include "HAL_AVR_APM2_Class.h"
 
diff --git a/libraries/AP_HAL_AVR/HAL_AVR_APM2_Class.h b/libraries/AP_HAL_AVR/HAL_AVR_APM2_Class.h
index ddadbc6bd6..b8428b85df 100644
--- a/libraries/AP_HAL_AVR/HAL_AVR_APM2_Class.h
+++ b/libraries/AP_HAL_AVR/HAL_AVR_APM2_Class.h
@@ -2,14 +2,14 @@
 #ifndef __AP_HAL_AVR_APM2_HAL_AVR_H__
 #define __AP_HAL_AVR_APM2_HAL_AVR_H__
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 
 /* To save linker space, we need to make sure the HAL_AVR_APM2 class
  * is built iff we are building for HAL_BOARD_APM2. These defines must
  * wrap the whole HAL_AVR_APM2 class declaration and definition. */
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM2
 
-#include <AP_HAL_AVR.h>
+#include "AP_HAL_AVR.h"
 #include "AP_HAL_AVR_Namespace.h"
 
 /**
diff --git a/libraries/AP_HAL_AVR/I2CDriver.cpp b/libraries/AP_HAL_AVR/I2CDriver.cpp
index 27db9e5800..a511a7fd05 100644
--- a/libraries/AP_HAL_AVR/I2CDriver.cpp
+++ b/libraries/AP_HAL_AVR/I2CDriver.cpp
@@ -33,7 +33,7 @@
  *
  */
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #if (CONFIG_HAL_BOARD == HAL_BOARD_APM1 || CONFIG_HAL_BOARD == HAL_BOARD_APM2)
 
 #include <inttypes.h>
@@ -41,7 +41,7 @@
 #include <avr/io.h>
 #include <avr/interrupt.h>
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #include "I2CDriver.h"
 using namespace AP_HAL_AVR;
 
diff --git a/libraries/AP_HAL_AVR/I2CDriver.h b/libraries/AP_HAL_AVR/I2CDriver.h
index 53b9aeac5a..2b0962e7f3 100644
--- a/libraries/AP_HAL_AVR/I2CDriver.h
+++ b/libraries/AP_HAL_AVR/I2CDriver.h
@@ -2,7 +2,7 @@
 #ifndef __AP_HAL_AVR_I2C_DRIVER_H__
 #define __AP_HAL_AVR_I2C_DRIVER_H__
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #include "AP_HAL_AVR_Namespace.h"
 
 #define AVRI2CDRIVER_MAX_BUFFER_SIZE 32
diff --git a/libraries/AP_HAL_AVR/RCInput.h b/libraries/AP_HAL_AVR/RCInput.h
index 1df15b742a..36ac5423f0 100644
--- a/libraries/AP_HAL_AVR/RCInput.h
+++ b/libraries/AP_HAL_AVR/RCInput.h
@@ -2,7 +2,7 @@
 #ifndef __AP_HAL_AVR_RC_INPUT_H__
 #define __AP_HAL_AVR_RC_INPUT_H__
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #include "AP_HAL_AVR_Namespace.h"
 
 #define AVR_RC_INPUT_NUM_CHANNELS 11
diff --git a/libraries/AP_HAL_AVR/RCInput_APM1.cpp b/libraries/AP_HAL_AVR/RCInput_APM1.cpp
index 9395ccd7da..83adb89b7c 100644
--- a/libraries/AP_HAL_AVR/RCInput_APM1.cpp
+++ b/libraries/AP_HAL_AVR/RCInput_APM1.cpp
@@ -1,11 +1,11 @@
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #if (CONFIG_HAL_BOARD == HAL_BOARD_APM1 || CONFIG_HAL_BOARD == HAL_BOARD_APM2)
 
 #include <avr/io.h>
 #include <avr/interrupt.h>
 
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
+#include <AP_HAL/AP_HAL.h>
+#include "AP_HAL_AVR.h"
 #include "RCInput.h"
 #include "utility/ISRRegistry.h"
 using namespace AP_HAL;
diff --git a/libraries/AP_HAL_AVR/RCInput_APM2.cpp b/libraries/AP_HAL_AVR/RCInput_APM2.cpp
index 1389fefb61..295b7a4f72 100644
--- a/libraries/AP_HAL_AVR/RCInput_APM2.cpp
+++ b/libraries/AP_HAL_AVR/RCInput_APM2.cpp
@@ -1,11 +1,11 @@
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #if (CONFIG_HAL_BOARD == HAL_BOARD_APM1 || CONFIG_HAL_BOARD == HAL_BOARD_APM2)
 
 #include <avr/io.h>
 #include <avr/interrupt.h>
 
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
+#include <AP_HAL/AP_HAL.h>
+#include "AP_HAL_AVR.h"
 #include "RCInput.h"
 #include "utility/ISRRegistry.h"
 using namespace AP_HAL;
diff --git a/libraries/AP_HAL_AVR/RCOutput.h b/libraries/AP_HAL_AVR/RCOutput.h
index c81e370505..ee5cafbaaa 100644
--- a/libraries/AP_HAL_AVR/RCOutput.h
+++ b/libraries/AP_HAL_AVR/RCOutput.h
@@ -2,7 +2,7 @@
 #ifndef __AP_HAL_AVR_RC_OUTPUT_H__
 #define __AP_HAL_AVR_RC_OUTPUT_H__
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #include "AP_HAL_AVR_Namespace.h"
 
 class AP_HAL_AVR::APM1RCOutput : public AP_HAL::RCOutput {
diff --git a/libraries/AP_HAL_AVR/RCOutput_APM1.cpp b/libraries/AP_HAL_AVR/RCOutput_APM1.cpp
index 9d5da0ccc7..2b5e17f6df 100644
--- a/libraries/AP_HAL_AVR/RCOutput_APM1.cpp
+++ b/libraries/AP_HAL_AVR/RCOutput_APM1.cpp
@@ -1,10 +1,10 @@
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM1
 
 #include <avr/interrupt.h>
 
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
+#include <AP_HAL/AP_HAL.h>
+#include "AP_HAL_AVR.h"
 #include "RCOutput.h"
 using namespace AP_HAL_AVR;
 
diff --git a/libraries/AP_HAL_AVR/RCOutput_APM2.cpp b/libraries/AP_HAL_AVR/RCOutput_APM2.cpp
index 9993f91308..e2f2f7623d 100644
--- a/libraries/AP_HAL_AVR/RCOutput_APM2.cpp
+++ b/libraries/AP_HAL_AVR/RCOutput_APM2.cpp
@@ -1,10 +1,10 @@
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM2
 
 #include <avr/interrupt.h>
 
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
+#include <AP_HAL/AP_HAL.h>
+#include "AP_HAL_AVR.h"
 #include "RCOutput.h"
 using namespace AP_HAL_AVR;
 
diff --git a/libraries/AP_HAL_AVR/SPIDeviceManager_APM1.cpp b/libraries/AP_HAL_AVR/SPIDeviceManager_APM1.cpp
index e7406f89df..84a8322f49 100644
--- a/libraries/AP_HAL_AVR/SPIDeviceManager_APM1.cpp
+++ b/libraries/AP_HAL_AVR/SPIDeviceManager_APM1.cpp
@@ -1,8 +1,8 @@
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM1
 
 #include <avr/io.h>
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #include "SPIDriver.h"
 #include "SPIDevices.h"
 #include "GPIO.h"
diff --git a/libraries/AP_HAL_AVR/SPIDeviceManager_APM2.cpp b/libraries/AP_HAL_AVR/SPIDeviceManager_APM2.cpp
index 397bf3eff2..a343d01045 100644
--- a/libraries/AP_HAL_AVR/SPIDeviceManager_APM2.cpp
+++ b/libraries/AP_HAL_AVR/SPIDeviceManager_APM2.cpp
@@ -1,8 +1,8 @@
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM2
 
 #include <avr/io.h>
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #include "SPIDriver.h"
 #include "SPIDevices.h"
 #include "utility/pins_arduino_mega.h"
diff --git a/libraries/AP_HAL_AVR/SPIDevice_SPI0.cpp b/libraries/AP_HAL_AVR/SPIDevice_SPI0.cpp
index 22a3956c02..304e5333bf 100644
--- a/libraries/AP_HAL_AVR/SPIDevice_SPI0.cpp
+++ b/libraries/AP_HAL_AVR/SPIDevice_SPI0.cpp
@@ -1,9 +1,9 @@
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #if (CONFIG_HAL_BOARD == HAL_BOARD_APM1 || CONFIG_HAL_BOARD == HAL_BOARD_APM2)
 
 #include <avr/io.h>
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #include "SPIDevices.h"
 #include "GPIO.h"
 #include "Semaphores.h"
diff --git a/libraries/AP_HAL_AVR/SPIDevice_SPI2.cpp b/libraries/AP_HAL_AVR/SPIDevice_SPI2.cpp
index 4c4b5f78f1..6344fb2624 100644
--- a/libraries/AP_HAL_AVR/SPIDevice_SPI2.cpp
+++ b/libraries/AP_HAL_AVR/SPIDevice_SPI2.cpp
@@ -1,10 +1,10 @@
 /// -*- tab-width: 4; Mode: C++; c-basic-offset: 4; indent-tabs-mode: nil -*-
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #if (CONFIG_HAL_BOARD == HAL_BOARD_APM1 || CONFIG_HAL_BOARD == HAL_BOARD_APM2)
 
 #include <avr/io.h>
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #include "SPIDevices.h"
 #include "GPIO.h"
 #include "Semaphores.h"
diff --git a/libraries/AP_HAL_AVR/SPIDevice_SPI3.cpp b/libraries/AP_HAL_AVR/SPIDevice_SPI3.cpp
index 5ba5f2fd04..ef63199d1a 100644
--- a/libraries/AP_HAL_AVR/SPIDevice_SPI3.cpp
+++ b/libraries/AP_HAL_AVR/SPIDevice_SPI3.cpp
@@ -1,11 +1,11 @@
 /// -*- tab-width: 4; Mode: C++; c-basic-offset: 4; indent-tabs-mode: nil -*-
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #if (CONFIG_HAL_BOARD == HAL_BOARD_APM1 || CONFIG_HAL_BOARD == HAL_BOARD_APM2)
 
 
 #include <avr/io.h>
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #include "SPIDevices.h"
 #include "GPIO.h"
 #include "Semaphores.h"
diff --git a/libraries/AP_HAL_AVR/SPIDevices.h b/libraries/AP_HAL_AVR/SPIDevices.h
index c4f24defd9..46adcb4074 100644
--- a/libraries/AP_HAL_AVR/SPIDevices.h
+++ b/libraries/AP_HAL_AVR/SPIDevices.h
@@ -2,7 +2,7 @@
 #ifndef __AP_HAL_AVR_SPI_DEVICES_H__
 #define __AP_HAL_AVR_SPI_DEVICES_H__
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #include "AP_HAL_AVR_Namespace.h"
 
 class AP_HAL_AVR::AVRSPI0DeviceDriver : public AP_HAL::SPIDeviceDriver {
diff --git a/libraries/AP_HAL_AVR/SPIDriver.h b/libraries/AP_HAL_AVR/SPIDriver.h
index abe5825290..fe3ea34b92 100644
--- a/libraries/AP_HAL_AVR/SPIDriver.h
+++ b/libraries/AP_HAL_AVR/SPIDriver.h
@@ -2,7 +2,7 @@
 #ifndef __AP_HAL_AVR_SPI_DRIVER_H__
 #define __AP_HAL_AVR_SPI_DRIVER_H__
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #include "AP_HAL_AVR_Namespace.h"
 #include "GPIO.h"
 #include "SPIDevices.h"
diff --git a/libraries/AP_HAL_AVR/Scheduler.cpp b/libraries/AP_HAL_AVR/Scheduler.cpp
index ec04efbbf9..cf922340ad 100644
--- a/libraries/AP_HAL_AVR/Scheduler.cpp
+++ b/libraries/AP_HAL_AVR/Scheduler.cpp
@@ -1,6 +1,6 @@
 /// -*- tab-width: 4; Mode: C++; c-basic-offset: 4; indent-tabs-mode: nil -*-
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #if (CONFIG_HAL_BOARD == HAL_BOARD_APM1 || CONFIG_HAL_BOARD == HAL_BOARD_APM2)
 
 #include <avr/io.h>
diff --git a/libraries/AP_HAL_AVR/Scheduler.h b/libraries/AP_HAL_AVR/Scheduler.h
index 3ccbd9f729..8aadff6236 100644
--- a/libraries/AP_HAL_AVR/Scheduler.h
+++ b/libraries/AP_HAL_AVR/Scheduler.h
@@ -2,7 +2,7 @@
 #ifndef __AP_HAL_AVR_SCHEDULER_H__
 #define __AP_HAL_AVR_SCHEDULER_H__
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #include "AP_HAL_AVR_Namespace.h"
 
 #define AVR_SCHEDULER_MAX_TIMER_PROCS 4
diff --git a/libraries/AP_HAL_AVR/Scheduler_Timer.cpp b/libraries/AP_HAL_AVR/Scheduler_Timer.cpp
index d73d450c2e..a3bc24818c 100644
--- a/libraries/AP_HAL_AVR/Scheduler_Timer.cpp
+++ b/libraries/AP_HAL_AVR/Scheduler_Timer.cpp
@@ -1,4 +1,4 @@
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #if (CONFIG_HAL_BOARD == HAL_BOARD_APM1 || CONFIG_HAL_BOARD == HAL_BOARD_APM2)
 
 #include <avr/io.h>
diff --git a/libraries/AP_HAL_AVR/Semaphores.cpp b/libraries/AP_HAL_AVR/Semaphores.cpp
index 8e77fbbf1c..1852d92b26 100644
--- a/libraries/AP_HAL_AVR/Semaphores.cpp
+++ b/libraries/AP_HAL_AVR/Semaphores.cpp
@@ -1,13 +1,13 @@
 /// -*- tab-width: 4; Mode: C++; c-basic-offset: 4; indent-tabs-mode: nil -*-
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 
 #if (CONFIG_HAL_BOARD == HAL_BOARD_APM1 || CONFIG_HAL_BOARD == HAL_BOARD_APM2)
 
 #include <avr/io.h>
 #include <avr/interrupt.h>
 
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
+#include <AP_HAL/AP_HAL.h>
+#include "AP_HAL_AVR.h"
 #include "Semaphores.h"
 #include "Scheduler.h"
 using namespace AP_HAL_AVR;
diff --git a/libraries/AP_HAL_AVR/Semaphores.h b/libraries/AP_HAL_AVR/Semaphores.h
index 8b30bd8f29..1d00ffd651 100644
--- a/libraries/AP_HAL_AVR/Semaphores.h
+++ b/libraries/AP_HAL_AVR/Semaphores.h
@@ -2,8 +2,8 @@
 #ifndef __AP_HAL_AVR_SEMAPHORES_H__
 #define __AP_HAL_AVR_SEMAPHORES_H__
 
-#include <AP_HAL.h>
-#include <AP_HAL_AVR_Namespace.h>
+#include <AP_HAL/AP_HAL.h>
+#include "AP_HAL_AVR_Namespace.h"
 
 class AP_HAL_AVR::AVRSemaphore : public AP_HAL::Semaphore {
 public:
diff --git a/libraries/AP_HAL_AVR/Storage.cpp b/libraries/AP_HAL_AVR/Storage.cpp
index c108db23ac..36d5323a72 100644
--- a/libraries/AP_HAL_AVR/Storage.cpp
+++ b/libraries/AP_HAL_AVR/Storage.cpp
@@ -1,4 +1,4 @@
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #if (CONFIG_HAL_BOARD == HAL_BOARD_APM1 || CONFIG_HAL_BOARD == HAL_BOARD_APM2)
 
 #include <avr/io.h>
diff --git a/libraries/AP_HAL_AVR/Storage.h b/libraries/AP_HAL_AVR/Storage.h
index 141478071f..67e662f8a1 100644
--- a/libraries/AP_HAL_AVR/Storage.h
+++ b/libraries/AP_HAL_AVR/Storage.h
@@ -3,7 +3,7 @@
 #ifndef __AP_HAL_AVR_STORAGE_H__
 #define __AP_HAL_AVR_STORAGE_H__
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #include "AP_HAL_AVR_Namespace.h"
 
 class AP_HAL_AVR::AVREEPROMStorage : public AP_HAL::Storage {
diff --git a/libraries/AP_HAL_AVR/UARTDriver.cpp b/libraries/AP_HAL_AVR/UARTDriver.cpp
index e9276a1cba..fdccb2d451 100644
--- a/libraries/AP_HAL_AVR/UARTDriver.cpp
+++ b/libraries/AP_HAL_AVR/UARTDriver.cpp
@@ -17,7 +17,7 @@
 //
 //      Copyright (c) 2010 Michael Smith. All rights reserved.
 //
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #if (CONFIG_HAL_BOARD == HAL_BOARD_APM1 || CONFIG_HAL_BOARD == HAL_BOARD_APM2)
 
 #include <limits.h>
@@ -26,8 +26,8 @@
 
 #include <avr/pgmspace.h>
 
-#include <AP_HAL.h>
-#include <AP_Math.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_Math/AP_Math.h>
 #include "UARTDriver.h"
 
 using namespace AP_HAL_AVR;
diff --git a/libraries/AP_HAL_AVR/UARTDriver.h b/libraries/AP_HAL_AVR/UARTDriver.h
index e4338735df..0dfb8f60c9 100644
--- a/libraries/AP_HAL_AVR/UARTDriver.h
+++ b/libraries/AP_HAL_AVR/UARTDriver.h
@@ -1,7 +1,7 @@
 
 #ifndef __AP_HAL_AVR_UART_DRIVER_H__
 #define __AP_HAL_AVR_UART_DRIVER_H__
-#include <AP_HAL_Boards.h>
+#include <AP_HAL/AP_HAL_Boards.h>
 #if (CONFIG_HAL_BOARD == HAL_BOARD_APM1 || CONFIG_HAL_BOARD == HAL_BOARD_APM2)
 
 #include <stdint.h>
@@ -9,7 +9,7 @@
 
 #include <avr/interrupt.h>
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #include "AP_HAL_AVR_Namespace.h"
 
 /**
diff --git a/libraries/AP_HAL_AVR/Util.h b/libraries/AP_HAL_AVR/Util.h
index 7b5277127d..3eee93cfa7 100644
--- a/libraries/AP_HAL_AVR/Util.h
+++ b/libraries/AP_HAL_AVR/Util.h
@@ -2,7 +2,7 @@
 #ifndef __AP_HAL_AVR_UTIL_H__
 #define __AP_HAL_AVR_UTIL_H__
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #include "AP_HAL_AVR_Namespace.h"
 #include "memcheck.h"
 
diff --git a/libraries/AP_HAL_AVR/examples/ArduCopterLibs/ArduCopterLibs.cpp b/libraries/AP_HAL_AVR/examples/ArduCopterLibs/ArduCopterLibs.cpp
index 49abec4f9c..26a65aea54 100644
--- a/libraries/AP_HAL_AVR/examples/ArduCopterLibs/ArduCopterLibs.cpp
+++ b/libraries/AP_HAL_AVR/examples/ArduCopterLibs/ArduCopterLibs.cpp
@@ -1,48 +1,48 @@
 
-#include <AP_Common.h>
-#include <AP_Progmem.h>
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.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_Common.h>
-#include <AP_Progmem.h>
-#include <AP_Menu.h>
-#include <AP_Param.h>
-#include <AP_GPS.h>             // ArduPilot GPS library
-#include <AP_ADC.h>             // ArduPilot Mega Analog to Digital Converter Library
-#include <AP_Baro.h>
-#include <AP_Declination.h>
-#include <AP_Compass.h>         // ArduPilot Mega Magnetometer Library
-#include <AP_Math.h>            // ArduPilot Mega Vector/Matrix math Library
-#include <AP_Curve.h>           // Curve used to linearlise throttle pwm to thrust
-#include <AP_InertialSensor.h>  // ArduPilot Mega Inertial Sensor (accel & gyro) Library
+#include <AP_Common/AP_Common.h>
+#include <AP_Progmem/AP_Progmem.h>
+#include <AP_Menu/AP_Menu.h>
+#include <AP_Param/AP_Param.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_Baro/AP_Baro.h>
+#include <AP_Declination/AP_Declination.h>
+#include <AP_Compass/AP_Compass.h>         // ArduPilot Mega Magnetometer Library
+#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_InertialSensor/AP_InertialSensor.h>  // ArduPilot Mega Inertial Sensor (accel & gyro) Library
                                 // (only included for makefile libpath to work)
-#include <AP_AHRS.h>
-#include <AC_PID.h>             // PID library
-#include <AC_P.h>               // P library
-#include <RC_Channel.h>         // RC Channel Library
-#include <AP_Motors.h>          // AP Motors library
-#include <AP_ADC_AnalogSource.h>
-#include <AP_RangeFinder.h>     // Range finder library
-#include <AP_OpticalFlow.h>     // Optical Flow library
-#include <Filter.h>             // Filter library
-#include <AP_Buffer.h>          // APM FIFO Buffer
-#include <AP_Relay.h>           // APM relay
-#include <AP_Camera.h>          // Photo or video camera
-#include <AP_Mount.h>           // Camera/Antenna mount
-#include <AP_Airspeed.h>        // needed for AHRS build
-#include <AP_Vehicle.h>         // needed for AHRS build
-#include <AP_Notify.h>
-#include <DataFlash.h>
-#include <AP_InertialNav.h>     // ArduPilot Mega inertial navigation library
-#include <GCS_MAVLink.h>
-#include <AP_Mission.h>
-#include <StorageManager.h>
-#include <AP_Terrain.h>
-#include <memcheck.h>
-#include <AP_NavEKF.h>
-#include <AP_Nav_Common.h>
-#include <AP_BattMonitor.h>
+#include <AP_AHRS/AP_AHRS.h>
+#include <AC_PID/AC_PID.h>             // PID library
+#include <AC_PID/AC_P.h>               // P library
+#include <RC_Channel/RC_Channel.h>         // RC Channel Library
+#include <AP_Motors/AP_Motors.h>          // AP Motors library
+#include <AP_ADC_AnalogSource/AP_ADC_AnalogSource.h>
+#include <AP_RangeFinder/AP_RangeFinder.h>     // Range finder library
+#include <AP_OpticalFlow/AP_OpticalFlow.h>     // Optical Flow library
+#include <Filter/Filter.h>             // Filter library
+#include <AP_Buffer/AP_Buffer.h>          // APM FIFO Buffer
+#include <AP_Relay/AP_Relay.h>           // APM relay
+#include <AP_Camera/AP_Camera.h>          // Photo or video camera
+#include <AP_Mount/AP_Mount.h>           // Camera/Antenna mount
+#include <AP_Airspeed/AP_Airspeed.h>        // needed for AHRS build
+#include <AP_Vehicle/AP_Vehicle.h>         // needed for AHRS build
+#include <AP_Notify/AP_Notify.h>
+#include <DataFlash/DataFlash.h>
+#include <AP_InertialNav/AP_InertialNav.h>     // ArduPilot Mega inertial navigation library
+#include <GCS_MAVLink/GCS_MAVLink.h>
+#include <AP_Mission/AP_Mission.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_Terrain/AP_Terrain.h>
+#include <AP_HAL_AVR/memcheck.h>
+#include <AP_NavEKF/AP_NavEKF.h>
+#include <AP_NavEKF/AP_Nav_Common.h>
+#include <AP_BattMonitor/AP_BattMonitor.h>
 
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM2
 const AP_HAL::HAL& hal = AP_HAL_AVR_APM2;
diff --git a/libraries/AP_HAL_AVR/examples/ArduPlaneLibs/ArduPlaneLibs.cpp b/libraries/AP_HAL_AVR/examples/ArduPlaneLibs/ArduPlaneLibs.cpp
index c01200cb53..3e3752581f 100644
--- a/libraries/AP_HAL_AVR/examples/ArduPlaneLibs/ArduPlaneLibs.cpp
+++ b/libraries/AP_HAL_AVR/examples/ArduPlaneLibs/ArduPlaneLibs.cpp
@@ -1,42 +1,42 @@
 
 
 // Libraries
-#include <AP_Common.h>
-#include <AP_Progmem.h>
-#include <AP_Menu.h>
-#include <AP_Param.h>
-#include <AP_GPS.h>         // ArduPilot GPS library
-#include <AP_Baro.h>        // ArduPilot barometer library
-#include <AP_Compass.h>     // ArduPilot Mega Magnetometer Library
-#include <AP_Math.h>        // ArduPilot Mega Vector/Matrix math Library
-#include <AP_ADC.h>         // ArduPilot Mega Analog to Digital Converter Library
-#include <AP_InertialSensor.h> // Inertial Sensor Library
-#include <AP_AHRS.h>         // ArduPilot Mega DCM Library
-#include <PID.h>            // PID library
-#include <RC_Channel.h>     // RC Channel Library
-#include <AP_ADC_AnalogSource.h>
-#include <AP_RangeFinder.h>     // Range finder library
-#include <Filter.h>                     // Filter library
-#include <AP_Buffer.h>      // APM FIFO Buffer
-#include <AP_Relay.h>       // APM relay
-#include <AP_Camera.h>          // Photo or video camera
-#include <AP_Airspeed.h>
-#include <AP_Notify.h>
-#include <memcheck.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Progmem/AP_Progmem.h>
+#include <AP_Menu/AP_Menu.h>
+#include <AP_Param/AP_Param.h>
+#include <AP_GPS/AP_GPS.h>         // ArduPilot GPS library
+#include <AP_Baro/AP_Baro.h>        // ArduPilot barometer library
+#include <AP_Compass/AP_Compass.h>     // ArduPilot Mega Magnetometer Library
+#include <AP_Math/AP_Math.h>        // ArduPilot Mega Vector/Matrix math Library
+#include <AP_ADC/AP_ADC.h>         // ArduPilot Mega Analog to Digital Converter Library
+#include <AP_InertialSensor/AP_InertialSensor.h> // Inertial Sensor Library
+#include <AP_AHRS/AP_AHRS.h>         // ArduPilot Mega DCM Library
+#include <PID/PID.h>            // PID library
+#include <RC_Channel/RC_Channel.h>     // RC Channel Library
+#include <AP_ADC_AnalogSource/AP_ADC_AnalogSource.h>
+#include <AP_RangeFinder/AP_RangeFinder.h>     // Range finder library
+#include <Filter/Filter.h>                     // Filter library
+#include <AP_Buffer/AP_Buffer.h>      // APM FIFO Buffer
+#include <AP_Relay/AP_Relay.h>       // APM relay
+#include <AP_Camera/AP_Camera.h>          // Photo or video camera
+#include <AP_Airspeed/AP_Airspeed.h>
+#include <AP_Notify/AP_Notify.h>
+#include <AP_HAL_AVR/memcheck.h>
 
-#include <DataFlash.h>
-#include <APM_Control.h>
-#include <AP_Vehicle.h>
-#include <GCS_MAVLink.h>    // MAVLink GCS definitions
-#include <AP_Mission.h>
-#include <StorageManager.h>
-#include <AP_Terrain.h>
-#include <AP_Mount.h>           // Camera/Antenna mount
-#include <AP_Declination.h> // ArduPilot Mega Declination Helper Library
-#include <AP_BattMonitor.h>
+#include <DataFlash/DataFlash.h>
+#include <APM_Control/APM_Control.h>
+#include <AP_Vehicle/AP_Vehicle.h>
+#include <GCS_MAVLink/GCS_MAVLink.h>    // MAVLink GCS definitions
+#include <AP_Mission/AP_Mission.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_Terrain/AP_Terrain.h>
+#include <AP_Mount/AP_Mount.h>           // Camera/Antenna mount
+#include <AP_Declination/AP_Declination.h> // ArduPilot Mega Declination Helper Library
+#include <AP_BattMonitor/AP_BattMonitor.h>
 
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
 
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM2
 const AP_HAL::HAL& hal = AP_HAL_AVR_APM2;
diff --git a/libraries/AP_HAL_AVR/examples/Blink/Blink.cpp b/libraries/AP_HAL_AVR/examples/Blink/Blink.cpp
index 53cbb2de1b..650960c94e 100644
--- a/libraries/AP_HAL_AVR/examples/Blink/Blink.cpp
+++ b/libraries/AP_HAL_AVR/examples/Blink/Blink.cpp
@@ -1,12 +1,12 @@
 
-#include <AP_Common.h>
-#include <AP_Math.h>
-#include <AP_Param.h>
-#include <StorageManager.h>
-#include <AP_Progmem.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Math/AP_Math.h>
+#include <AP_Param/AP_Param.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_Progmem/AP_Progmem.h>
 
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
 
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM1
 const AP_HAL::HAL& hal = AP_HAL_AVR_APM1;
diff --git a/libraries/AP_HAL_AVR/examples/Console/Console.cpp b/libraries/AP_HAL_AVR/examples/Console/Console.cpp
index 748cb3a19c..0a8d08966b 100644
--- a/libraries/AP_HAL_AVR/examples/Console/Console.cpp
+++ b/libraries/AP_HAL_AVR/examples/Console/Console.cpp
@@ -6,14 +6,14 @@
 // This code is placed into the public domain.
 //
 
-#include <AP_Common.h>
-#include <AP_Math.h>
-#include <AP_Param.h>
-#include <StorageManager.h>
-#include <AP_Progmem.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Math/AP_Math.h>
+#include <AP_Param/AP_Param.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_Progmem/AP_Progmem.h>
 
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
 
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM2
 const AP_HAL::HAL& hal = AP_HAL_AVR_APM2;
diff --git a/libraries/AP_HAL_AVR/examples/I2CDriver_HMC5883L/I2CDriver_HMC5883L.cpp b/libraries/AP_HAL_AVR/examples/I2CDriver_HMC5883L/I2CDriver_HMC5883L.cpp
index 5d9b7392e6..310841ebd4 100644
--- a/libraries/AP_HAL_AVR/examples/I2CDriver_HMC5883L/I2CDriver_HMC5883L.cpp
+++ b/libraries/AP_HAL_AVR/examples/I2CDriver_HMC5883L/I2CDriver_HMC5883L.cpp
@@ -4,14 +4,14 @@
 *   the three axis of data.
 *******************************************/
 
-#include <AP_Common.h>
-#include <AP_Math.h>
-#include <AP_Param.h>
-#include <StorageManager.h>
-#include <AP_Progmem.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Math/AP_Math.h>
+#include <AP_Param/AP_Param.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_Progmem/AP_Progmem.h>
 
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
 
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM2
 const AP_HAL::HAL& hal = AP_HAL_AVR_APM2;
diff --git a/libraries/AP_HAL_AVR/examples/LCDTest/LCDTest.cpp b/libraries/AP_HAL_AVR/examples/LCDTest/LCDTest.cpp
index 2a49e4bbe4..ade72cb416 100644
--- a/libraries/AP_HAL_AVR/examples/LCDTest/LCDTest.cpp
+++ b/libraries/AP_HAL_AVR/examples/LCDTest/LCDTest.cpp
@@ -37,13 +37,13 @@
 
 // include the library code:
 
-#include <AP_Common.h>
-#include <AP_Math.h>
-#include <AP_Param.h>
-#include <AP_Progmem.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Math/AP_Math.h>
+#include <AP_Param/AP_Param.h>
+#include <AP_Progmem/AP_Progmem.h>
 
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
 
 #include "LCrystal.h"
 
diff --git a/libraries/AP_HAL_AVR/examples/LCDTest/LCrystal.cpp b/libraries/AP_HAL_AVR/examples/LCDTest/LCrystal.cpp
index 00ea2c904d..2d351e7746 100644
--- a/libraries/AP_HAL_AVR/examples/LCDTest/LCrystal.cpp
+++ b/libraries/AP_HAL_AVR/examples/LCDTest/LCrystal.cpp
@@ -4,7 +4,7 @@
 #include <string.h>
 #include <inttypes.h>
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 
 extern const AP_HAL::HAL& hal;
 
diff --git a/libraries/AP_HAL_AVR/examples/RCInputTest/RCInputTest.cpp b/libraries/AP_HAL_AVR/examples/RCInputTest/RCInputTest.cpp
index 5d192285ba..b46c982191 100644
--- a/libraries/AP_HAL_AVR/examples/RCInputTest/RCInputTest.cpp
+++ b/libraries/AP_HAL_AVR/examples/RCInputTest/RCInputTest.cpp
@@ -1,12 +1,12 @@
 
-#include <AP_Common.h>
-#include <AP_Math.h>
-#include <AP_Param.h>
-#include <StorageManager.h>
-#include <AP_Progmem.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Math/AP_Math.h>
+#include <AP_Param/AP_Param.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_Progmem/AP_Progmem.h>
 
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
 
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM2
 const AP_HAL::HAL& hal = AP_HAL_AVR_APM2;
diff --git a/libraries/AP_HAL_AVR/examples/RCJitterTest/RCJitterTest.cpp b/libraries/AP_HAL_AVR/examples/RCJitterTest/RCJitterTest.cpp
index 10e3bdffae..2bad9a043c 100644
--- a/libraries/AP_HAL_AVR/examples/RCJitterTest/RCJitterTest.cpp
+++ b/libraries/AP_HAL_AVR/examples/RCJitterTest/RCJitterTest.cpp
@@ -1,11 +1,11 @@
-#include <AP_Common.h>
-#include <AP_Math.h>
-#include <AP_Param.h>
-#include <StorageManager.h>
-#include <AP_Progmem.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Math/AP_Math.h>
+#include <AP_Param/AP_Param.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_Progmem/AP_Progmem.h>
 
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
 
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM2
 const AP_HAL::HAL& hal = AP_HAL_AVR_APM2;
diff --git a/libraries/AP_HAL_AVR/examples/RCPassthroughTest/RCPassthroughTest.cpp b/libraries/AP_HAL_AVR/examples/RCPassthroughTest/RCPassthroughTest.cpp
index 8bca2c20d4..78f52b1b92 100644
--- a/libraries/AP_HAL_AVR/examples/RCPassthroughTest/RCPassthroughTest.cpp
+++ b/libraries/AP_HAL_AVR/examples/RCPassthroughTest/RCPassthroughTest.cpp
@@ -1,12 +1,12 @@
 
-#include <AP_Common.h>
-#include <AP_Math.h>
-#include <AP_Param.h>
-#include <StorageManager.h>
-#include <AP_Progmem.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Math/AP_Math.h>
+#include <AP_Param/AP_Param.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_Progmem/AP_Progmem.h>
 
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
 
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM2
 const AP_HAL::HAL& hal = AP_HAL_AVR_APM2;
diff --git a/libraries/AP_HAL_AVR/examples/SPIDriver_MPU6000/SPIDriver_MPU6000.cpp b/libraries/AP_HAL_AVR/examples/SPIDriver_MPU6000/SPIDriver_MPU6000.cpp
index 442b1eca94..c7d35a238a 100644
--- a/libraries/AP_HAL_AVR/examples/SPIDriver_MPU6000/SPIDriver_MPU6000.cpp
+++ b/libraries/AP_HAL_AVR/examples/SPIDriver_MPU6000/SPIDriver_MPU6000.cpp
@@ -4,14 +4,14 @@
 *   temperature, three axis of gyro data
 *******************************************/
 
-#include <AP_Common.h>
-#include <AP_Math.h>
-#include <AP_Param.h>
-#include <StorageManager.h>
-#include <AP_Progmem.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Math/AP_Math.h>
+#include <AP_Param/AP_Param.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_Progmem/AP_Progmem.h>
 
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
 
 /* register #defines */
 #include "MPU6000.h"
diff --git a/libraries/AP_HAL_AVR/examples/Scheduler/Scheduler.cpp b/libraries/AP_HAL_AVR/examples/Scheduler/Scheduler.cpp
index f1169ba7cf..26e9f93698 100644
--- a/libraries/AP_HAL_AVR/examples/Scheduler/Scheduler.cpp
+++ b/libraries/AP_HAL_AVR/examples/Scheduler/Scheduler.cpp
@@ -1,11 +1,11 @@
 
-#include <AP_Common.h>
-#include <AP_Math.h>
-#include <AP_Param.h>
-#include <AP_Progmem.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Math/AP_Math.h>
+#include <AP_Param/AP_Param.h>
+#include <AP_Progmem/AP_Progmem.h>
 
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
 
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM2
 const AP_HAL::HAL& hal = AP_HAL_AVR_APM2;
diff --git a/libraries/AP_HAL_AVR/examples/Semaphore/Semaphore.cpp b/libraries/AP_HAL_AVR/examples/Semaphore/Semaphore.cpp
index af1f4d0c3e..e9fef7c6f1 100644
--- a/libraries/AP_HAL_AVR/examples/Semaphore/Semaphore.cpp
+++ b/libraries/AP_HAL_AVR/examples/Semaphore/Semaphore.cpp
@@ -1,10 +1,10 @@
-#include <AP_Common.h>
-#include <AP_Math.h>
-#include <AP_Param.h>
-#include <AP_Progmem.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Math/AP_Math.h>
+#include <AP_Param/AP_Param.h>
+#include <AP_Progmem/AP_Progmem.h>
 
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
 
 const AP_HAL::HAL& hal = AP_HAL_BOARD_DRIVER;
 
diff --git a/libraries/AP_HAL_AVR/examples/Storage/Storage.cpp b/libraries/AP_HAL_AVR/examples/Storage/Storage.cpp
index 67ae066603..0d012effcb 100644
--- a/libraries/AP_HAL_AVR/examples/Storage/Storage.cpp
+++ b/libraries/AP_HAL_AVR/examples/Storage/Storage.cpp
@@ -1,12 +1,12 @@
 
-#include <AP_Common.h>
-#include <AP_Math.h>
-#include <AP_Param.h>
-#include <StorageManager.h>
-#include <AP_Progmem.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Math/AP_Math.h>
+#include <AP_Param/AP_Param.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_Progmem/AP_Progmem.h>
 
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
 
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM2
 const AP_HAL::HAL& hal = AP_HAL_AVR_APM2;
diff --git a/libraries/AP_HAL_AVR/examples/UARTDriver/UARTDriver.cpp b/libraries/AP_HAL_AVR/examples/UARTDriver/UARTDriver.cpp
index c0679b3ef4..732c00c649 100644
--- a/libraries/AP_HAL_AVR/examples/UARTDriver/UARTDriver.cpp
+++ b/libraries/AP_HAL_AVR/examples/UARTDriver/UARTDriver.cpp
@@ -6,14 +6,14 @@
 // This code is placed into the public domain.
 //
 
-#include <AP_Common.h>
-#include <AP_Math.h>
-#include <AP_Param.h>
-#include <StorageManager.h>
-#include <AP_Progmem.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Math/AP_Math.h>
+#include <AP_Param/AP_Param.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_Progmem/AP_Progmem.h>
 
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
 
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM2
 const AP_HAL::HAL& hal = AP_HAL_AVR_APM2;
diff --git a/libraries/AP_HAL_AVR/examples/UtilityStringTest/UtilityStringTest.cpp b/libraries/AP_HAL_AVR/examples/UtilityStringTest/UtilityStringTest.cpp
index 1988968bb3..b1fb79047e 100644
--- a/libraries/AP_HAL_AVR/examples/UtilityStringTest/UtilityStringTest.cpp
+++ b/libraries/AP_HAL_AVR/examples/UtilityStringTest/UtilityStringTest.cpp
@@ -2,14 +2,14 @@
 
 #include <string.h>
 
-#include <AP_Common.h>
-#include <AP_Math.h>
-#include <AP_Param.h>
-#include <StorageManager.h>
-#include <AP_Progmem.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Math/AP_Math.h>
+#include <AP_Param/AP_Param.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_Progmem/AP_Progmem.h>
 
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
 
 const AP_HAL::HAL& hal = AP_HAL_BOARD_DRIVER;
 
diff --git a/libraries/AP_HAL_AVR/memcheck.cpp b/libraries/AP_HAL_AVR/memcheck.cpp
index 5ac4d6b58b..fccb0fb4bf 100644
--- a/libraries/AP_HAL_AVR/memcheck.cpp
+++ b/libraries/AP_HAL_AVR/memcheck.cpp
@@ -8,7 +8,7 @@
  *  of false positives with uninitialised stack variables
  */
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #include <stdlib.h>
 #include <stdint.h>
 
diff --git a/libraries/AP_HAL_AVR/utility/ISRRegistry.cpp b/libraries/AP_HAL_AVR/utility/ISRRegistry.cpp
index f58124a2c9..48185c14da 100644
--- a/libraries/AP_HAL_AVR/utility/ISRRegistry.cpp
+++ b/libraries/AP_HAL_AVR/utility/ISRRegistry.cpp
@@ -1,4 +1,4 @@
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 #if (CONFIG_HAL_BOARD == HAL_BOARD_APM1 || CONFIG_HAL_BOARD == HAL_BOARD_APM2)
 
 #include <stdlib.h>
diff --git a/libraries/AP_HAL_AVR/utility/ISRRegistry.h b/libraries/AP_HAL_AVR/utility/ISRRegistry.h
index 3940d2d16e..d3cc317eb6 100644
--- a/libraries/AP_HAL_AVR/utility/ISRRegistry.h
+++ b/libraries/AP_HAL_AVR/utility/ISRRegistry.h
@@ -3,8 +3,8 @@
 #ifndef __AP_HAL_AVR_ISR_REGISTRY_H__
 #define __AP_HAL_AVR_ISR_REGISTRY_H__
 
-#include <AP_HAL.h>
-#include "AP_HAL_AVR_Namespace.h"
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR_Namespace.h>
 
 #define ISR_REGISTRY_TIMER2_OVF  0
 #define ISR_REGISTRY_TIMER4_CAPT 1
diff --git a/libraries/AP_HAL_AVR/utility/pins_arduino_mega.cpp b/libraries/AP_HAL_AVR/utility/pins_arduino_mega.cpp
index fdb81c5f55..168c2b34ca 100644
--- a/libraries/AP_HAL_AVR/utility/pins_arduino_mega.cpp
+++ b/libraries/AP_HAL_AVR/utility/pins_arduino_mega.cpp
@@ -1,4 +1,4 @@
-#include <AP_HAL_Boards.h>
+#include <AP_HAL/AP_HAL_Boards.h>
 #if CONFIG_HAL_BOARD == HAL_BOARD_APM1 || CONFIG_HAL_BOARD == HAL_BOARD_APM2
 
 #include <avr/io.h>