diff --git a/ArduSub/Sub.h b/ArduSub/Sub.h
index ac886965c0..df80024536 100644
--- a/ArduSub/Sub.h
+++ b/ArduSub/Sub.h
@@ -88,6 +88,18 @@
 #include <AP_BattMonitor/AP_BattMonitor.h>     // Battery monitor library
 #include <AP_BoardConfig/AP_BoardConfig.h>     // board configuration library
 #include <AP_Frsky_Telem/AP_Frsky_Telem.h>
+#include <AP_LandingGear/AP_LandingGear.h>     // Landing Gear library
+#include <AP_Terrain/AP_Terrain.h>
+#include <AP_ADSB/AP_ADSB.h>
+#include <AP_RPM/AP_RPM.h>
+#include <AC_InputManager/AC_InputManager.h>        // Pilot input handling library
+#include <AC_InputManager/AC_InputManager_Heli.h>   // Heli specific pilot input handling library
+
+// Configuration
+#include "defines.h"
+#include "config.h"
+
+// libraries which are dependent on #defines in defines.h and/or config.h
 #if SPRAYER == ENABLED
 #include <AC_Sprayer/AC_Sprayer.h>         // crop sprayer library
 #endif
@@ -97,23 +109,10 @@
 #if PARACHUTE == ENABLED
 #include <AP_Parachute/AP_Parachute.h>       // Parachute release library
 #endif
-#include <AP_LandingGear/AP_LandingGear.h>     // Landing Gear library
-#include <AP_Terrain/AP_Terrain.h>
-#include <AP_ADSB/AP_ADSB.h>
-#include <AP_RPM/AP_RPM.h>
 #if PRECISION_LANDING == ENABLED
 #include <AC_PrecLand/AC_PrecLand.h>
 #include <AP_IRLock/AP_IRLock.h>
 #endif
-#include <AC_InputManager/AC_InputManager.h>        // Pilot input handling library
-#include <AC_InputManager/AC_InputManager_Heli.h>   // Heli specific pilot input handling library
-
-
-// AP_HAL to Arduino compatibility layer
-// Configuration
-#include "defines.h"
-#include "config.h"
-#include "config_channels.h"
 
 // Local modules
 #include "Parameters.h"
diff --git a/ArduSub/config.h b/ArduSub/config.h
index 1c00da0331..37f9ea721c 100644
--- a/ArduSub/config.h
+++ b/ArduSub/config.h
@@ -27,11 +27,7 @@
 /// DO NOT EDIT THIS INCLUDE - if you want to make a local change, make that
 /// change in your local copy of APM_Config.h.
 ///
-#ifdef USE_CMAKE_APM_CONFIG
- #include "APM_Config_cmake.h"  // <== Prefer cmake config if it exists
-#else
- #include "APM_Config.h" // <== THIS INCLUDE, DO NOT EDIT IT. EVER.
-#endif
+#include "APM_Config.h" // <== THIS INCLUDE, DO NOT EDIT IT. EVER.
 
 
 //////////////////////////////////////////////////////////////////////////////
diff --git a/ArduSub/control_autotune.cpp b/ArduSub/control_autotune.cpp
index 1b9d7af73c..13777c850c 100644
--- a/ArduSub/control_autotune.cpp
+++ b/ArduSub/control_autotune.cpp
@@ -57,15 +57,15 @@
 #define AUTOTUNE_PI_RATIO_FOR_TESTING      0.1f     // I is set 10x smaller than P during testing
 #define AUTOTUNE_PI_RATIO_FINAL            1.0f     // I is set 1x P after testing
 #define AUTOTUNE_YAW_PI_RATIO_FINAL        0.1f     // I is set 1x P after testing
-#define AUTOTUNE_RD_MAX                  0.050f     // maximum Rate D value
+#define AUTOTUNE_RD_MAX                  0.200f     // maximum Rate D value
 #define AUTOTUNE_RLPF_MIN                  1.0f     // minimum Rate Yaw filter value
 #define AUTOTUNE_RLPF_MAX                  5.0f     // maximum Rate Yaw filter value
 #define AUTOTUNE_RP_MIN                   0.01f     // minimum Rate P value
 #define AUTOTUNE_RP_MAX                    2.0f     // maximum Rate P value
 #define AUTOTUNE_SP_MAX                   20.0f     // maximum Stab P value
 #define AUTOTUNE_SP_MIN                    0.5f     // maximum Stab P value
-#define AUTOTUNE_RP_ACCEL_MIN          36000.0f     // Minimum acceleration for Roll and Pitch
-#define AUTOTUNE_Y_ACCEL_MIN            9000.0f     // Minimum acceleration for Yaw
+#define AUTOTUNE_RP_ACCEL_MIN           4000.0f     // Minimum acceleration for Roll and Pitch
+#define AUTOTUNE_Y_ACCEL_MIN            1000.0f     // Minimum acceleration for Yaw
 #define AUTOTUNE_Y_FILT_FREQ              10.0f     // Autotune filter frequency when testing Yaw
 #define AUTOTUNE_SUCCESS_COUNT                4     // The number of successful iterations we need to freeze at current gains
 #define AUTOTUNE_D_UP_DOWN_MARGIN          0.2f     // The margin below the target that we tune D in