cc2538: clock: Request an etimer poll in clock_adjust()

During PM1+, the hardware timer used to implement the Contiki clock is frozen,
so clock_adjust() needs to be called when exiting those modes in order to
compensate for the clock ticks missed while the timer was frozen. Doing so
changes the Contiki clock time, so etimer_request_poll() needs to be called in
order to inform the etimer library that an etimer might have expired.

Note that waiting for the next clock ISR to call etimer_request_poll() is
unreliable because the system might go back to sleep beforehand.

Signed-off-by: Benoît Thébaudeau <benoit.thebaudeau@advansee.com>
cc2538: clock: Fix secs update in clock_adjust()

Whole elapsed seconds are added to secs first, so only the remaining subsecond
ticks should then be subtracted from second_countdown in order to decide whether
secs should be incremented again.

Otherwise, secs is not correctly updated in some cases, typically if the bit 7
of ticks is 1. E.g., with ticks = 128 (i.e. exactly 1 s elapsed) and
second_countdown = 128, secs was first incremented as expected, then 128 was
subtracted from second_countdown, giving 0 and triggering an unwanted second
increment of secs. Or with ticks = 129 (i.e. 1 s + 1 tick) and
second_countdown = 1, secs was first incremented as expected, then 129 was
subtracted from second_countdown, giving 128 and missing a second increment of
secs that should have occurred because second_countdown wrapped around.

Signed-off-by: Benoît Thébaudeau <benoit.thebaudeau@advansee.com>
cc2538: clock: Fix time drift occurring with PM1/2

The clock adjustments made when waking up from PM1/2 were very inaccurate. If
relying on ContikiMAC's rtimer to sleep, this led to Contiki's software clock
time, seconds and etimers to be 2.5 s slower after each min, i.e. 1 hour slower
after each day, which is a show stopper issue for most real-life applications.

This was caused by a lack of accuracy in several pieces of code during sleep
entry and wake-up:
 - It was difficult to synchronize the calls to RTIMER_NOW() before and after
   sleep with the deactivation and activation of the SysTick peripheral caused
   by PM1/2. This caused an inaccuracy in the corrective number of ticks passed
   to clock_adjust().
 - The value passed to clock_adjust() was truncated from an rtimer_clock_t
   value, but the accumulated error caused by these truncated bits was ignored.
 - The SysTick peripheral had to be stopped during the call to clock_adjust().

Rather than creating even more complicated clock adjustment mechanisms that
would probably still have mixed results as to accuracy, this change simply uses
the Sleep Timer counter as a base value for Contiki's clock and seconds
counters. The tick from the Systick peripheral is still used as the interrupt
source to update Contiki's clocks and timers. When running, the SysTick
peripheral and the Sleep Timer are synchronized, so combining both is not an
issue, and this allows not to alter the rtimer interrupt mechanism using the
Sleep Timer. The purpose of the Sleep Timer is to be an RTC, so it is the
perfect fit for the clock module, all the more it can not be disturbed by PM1/2.
If the 32-kHz XOSC is used, the Sleep Timer is also very accurate. If the
32-kHZ RCOSC is used, it is calibrated from the 32-MHz XOSC, so it is also
accurate, and the 32753-Hz vs. 32768-Hz systematic error in that case is
negligible, all the more one would use the 32-kHz XOSC for better accuracy.

Besides fixing this time drift issue, this change has several benefits:
 - clock_time(), clock_seconds() and RTIMER_NOW() start synchronized, and they
   change at the same source pace.
 - If clock_set_seconds() is called, then clock_seconds() indicates one more
   second almost exactly one second later, then exactly each second. Before this
   change, clock_seconds() was not synchronized with clock_set_seconds(), so the
   value returned by the former could be incremented immediately after the call
   to the latter in some cases.
 - The code tied to the clock module is simpler and more robust.

Signed-off-by: Benoît Thébaudeau <benoit.thebaudeau@advansee.com>
cc2538: Add adc driver and example

Signed-off-by: Benoît Thébaudeau <benoit.thebaudeau@advansee.com>
leds: Fix the API

The leds API did not work in some cases. E.g. with the following sequence:
  leds_off(LEDS_ALL);
  leds_toggle(LEDS_GREEN);
  leds_off(LEDS_ALL);
the green LED was remaining on after the last call.

This was caused by the toggle feature made synonymous with the invert feature,
although it is unrelated. leds_toggle() is indeed supposed to toggle an LED,
while leds_invert() is supposed to change the active level of an LED. However,
all users of leds_invert() actually meant leds_toggle(), and the invert feature
does not make sense in this module because it is not handy due to successive
calls to leds_invert() changing the intended behavior, and hardware active
levels should be managed in leds_arch_set() (e.g. by XORing the passed value
with a hardware-specific constant before setting the output levels of the pins).

Consequently, this change:
 - removes the leds_invert() function,
 - makes leds_toggle() behave as expected relatively to leds_off() / leds_on(),
 - sanitizes the code in the leds module.

Signed-off-by: Benoît Thébaudeau <benoit.thebaudeau@advansee.com>
leds: Add the leds_set() function

The leds_set() function is added on top of leds_arch_set() in order to have a
means of displaying a pattern on a set of LEDs, while keeping the ENERGEST
information up to date, which would be missing with a direct call to
leds_arch_set().

Signed-off-by: Benoît Thébaudeau <benoit.thebaudeau@advansee.com>
Fix PCAP packet header timestamp
Make the period for the uip-ds6 periodic task configurable
CC2538: add support for UART baudrate 9600, 38400 and 57600
Cooja: allow setting RSSI while sending and silence

It is now possible to set the RSSI while the radio is sending or when
no radiodata is received. This is now supported by all radiomediums
exept MRM. This also includes a GUI to configure the values.
Fix documentation
Fix backwards compatibility
cooja: interfaces/RimeAddress: renamed rimeaddr_node_addr to linkaddr_node_addr
cooja: plugins/Visualizer: Implemented mouse wheel zooming with mouse coordinates as center
[cooja] pluings/skings/UDGMVisualizerSkin: Replaced unclosable Box implementation of JSpinner menus by JInternalFrame based variant.
Merge pull request #566 from ejoerns/pull-req/addr-fix

[Cooja] rename rimeaddr_node_addr to linkaddr_node_addr in RimeAddress interface
Merge pull request #567 from ejoerns/pull-req/vis-scroll

[Cooja] Mouse wheel zooming for Visualizer
Merge pull request #568 from ejoerns/pull-req/cooja-udgmvis

[Cooja] Made UDGMVisualizerSkin closable
Merge pull request #565 from cmorty/pull/backwards

Fix backwards compatibility (and docs)
Merge pull request #533 from g-oikonomou/cooja-pcap-timestamp-fix

Fix Cooja PCAP packet header timestamps