AP_NavEKF : Reduce ripple in estimates that can cause copter motor 'pulsing'

This patch reduces the level of 5Hz and 10Hz 'pulsing' heard in motors
due to GPS and altimeter fusion which cause a small 5Hz and 10Hz ripple
on the output under some conditions. Attitude, velocity and position
state corrections from GPS, altimeter and magnetometer measurements are
applied incrementally in the interval from receiving the measurement to
the predicted time of receipt of the next measurement. Averaging of
attitude state corrections is not performed during periods of rapid
rotation.

Time stamps are now explicitly initialised to the current IMU time to
avoid unwanted activation of timeout logic on filter start and the
various calls to the hal.scheduler->millis() object have been
consolidated.

Unused variables have been removed