APM_Control: Modify D and I gain scaling
APM_Control: reduce the number of parameter saves in autotune

don't save a parameter unless it has changed by 0.1%
Copter: conditional yaw fix

waypoint command was setting auto_yaw_mode when it was run after the
do-cmd
yaw_look_at_heading was being set to current heading which was
overwriting the caller's desired heading
Mission: fix example sketch after GPS lib changes
Copter: bug fix for when WP_YAW_BEHAVIOR is 0
code style: add indentation rules for makefiles

(and remove some web file types that will probably never be in APM)
Copter: bug fix for conditional_distance command

Due to a race condition, the wp_distance was not being updated before
the conditional_distance
autotest: Added McMillan airstrip at Camp Roberts to locations.txt
AP_Rally library
AP_Rally: Minor fixes to AP_Rally after initial testing

- If a Rally point is being used, always respect the altitude set by the
user (don't take the max of that and the home point altitude).

- No need for constructor to pass in size of RallyLocation struct
Plane: Now using AP_Rally library.
Copter: integrate AP_Rally
Rally: define RALLY_WP_SIZE and RallyLocation
Common: remove RallyLocation defintion
Copter: remove RALLY_WP_SIZE definition
Plane: remove RALLY_WP_SIZE definition
Copter: bug fix AP_Rally param directory
AP_GPS: prevent writing GPS log headings multiple times
AP_NavEKF: fixed some matlab ! -> ~ typos

Pair-Programmed-With: Paul Riseborough <p_riseborough@live.com.au>
Replay: cope with too many log format msgs