[Makefile] add pcre lib to jsbsim, cleanup shell commands
[logalizer] fix missing tab in makefile
[jsbsim] ahrg, fix LDFLAGS
[gps] add gps_periodic_check to reset fix after timeout

- GpsIsLost should eventually be replaced by isLocal/GlobalCoordinateSystemValid from state interface

closes #637
[stm32] simplifly peripheral clock setup

There is now a convenience function in libopencm3 that makes the clock enable for peripherals easier across different STM families:
e.g.
rcc_periph_clock_enable(RCC_USART1);

closes #642
[stm32] ppm: remove extra gpio_enable_clock

not needed since this is already done in gpio_setup_pin_af
[boards] lisa_mx: fix alternate ppm input config
[sim] add dummy gpio function/macros in sim
[MF_DAQ] add power control with a gpio
[MF_DAQ] improve data logging (including MD5 and GPS)
[sim] send broadcasted messages to all aircraft

Previously, the broadcasted messages was no sent to the aircraft with the same ID.
I suppose this was to not send ACINFO to himself, but this should be
filtered by datalink parser in the end.
It also solves the rc_datalink issue in sim.
[sim] enabled downlink via ivy by default and rename var
[supervision] remove obsolete perl gui
[stm32] possibility to disable caret diagnostics on gcc 4.8
[ins] reset reference position from INS not from NAV

Nav is (almost) independent of the GPS which is a sensor and should only
be seen by the INS/AHRS subsystems.
It also allow to make shared INS filters more easily (example with
invariant filter).
Switched to using a compatible CFG-MSG format for newer ublox version (>=5)
[ins] cleaning and dox update to better match what it actually does
Replaced outdated CFG_MSG
[ins] remove hf|vf_realign from global ins struct

and fix some missing fuctions
[ins] remove ins_realign_v and ins_realign_h