AP_NavEKF : Fix bug in reset of position, height and velocity states

If the inertial solution velocity or position needs to be reset to the GPS or baro, the stored state history for the corresponding states should also be reset.
Otherwise the next GPS or baro measurement will be compared to an invalid previous state and will be rejected. This is particularly a problem if IMU saturation or timeout has occurred because the previous states could be out by a large amount
The position state should be reset to a GPS position corrected for velocity and measurement latency. This will make a noticeable difference for high speed flight vehicles, eg 11m at 50m/s.
AP_NavEKF : Fix bug in GPS innovation variance growth calculation

The uncertainty in acceleration is currently only scaled using horizontal accelerations, however during vertical plane aerobatics and high g pullups, misalignment in angles can cause significant horizontal acceleration error.
The scaling now uses the 3D acceleration vector length to better work during vertical plane high g maneouvres.
This error was found during flight testing with 8g pullups
AC_WPNav: add shift_wp_origin_to_current_pos for takeoff

This shifts the origin to the vehicle's current position and should be
called just before take-off to ensure there are no sudden roll or pitch
moves on takeoff.
Copter: shift pos targets to current location before takeoff
GPS: fix SIRF set-binary message

This fixes an issue in which the the update rate for the mediatek, which
uses a similar protocol, was not being set correctly
AP_NavEKF: simplify variable handling in EKF

use named state variables instead of states[] array where possible.
AP_NavEKF: make it clear that all sat counts are covered
AP_AHRS : add method to report if EKF is waiting to start
AHRS: rename ekfNotStarted method to initialised

Also created default implementation in AP_AHRS class so AP_AHRS_DCM does
not need to implement it.
Copter: only report ahrs unhealthy after initialisation
TradHeli: remove overall throttle level from landing check
AP_NavEKF : Fix bug in reset of GPS glitch offset

The GPS glitch offset was being zeroed during position resets. This caused the filter to reject subsequent GPS measurements if the GPS error persisted long enough to invoke a timeout and a position reset.
Copter: increase autotune limits

Rate D max to 0.020 (was 0.015)
Rate P max to 0.35 (was 0.25)
Stab P max to 20 (was 15)
Tri: _min_throttle interpreted as 0~1000 range for throttle_lower flag

limit.throttle_lower flag becomes true when the throttle passed into the
motors lib (which is in the 0 ~ 1000 range) is below _min throttle.
This makes the interpretation of the THR_MIN parameter consistent
between the main code (which uses 0 ~ 1000 range) and the motors lib
(which previously used the RC3_MIN ~ RC3_MAX range).
The remaining problem however is that the output of the motors continues
to use THR_MIN as if it were a pwm.  I don't believe this is a dangerous
problem however.
MotorsMatrix: _min_throttle interpreted as 0 ~ 1000 range for throttle_lower flag

Also trigger throttle_upper flag when throttle in reaches 1000
Copter: ReleaseNotes for AC3.2-rc11
Copter: version to AC3.2-rc11
Merge branch 'ArduCopter-3.2' of https://github.com/diydrones/ardupilot into output_filter
Copter: cleanup enabling of cli and frsky telem for APM
Copter: disable sonar on APM1 and TradHeli on APM2