Don't increment the counter when a button is pressed
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>
cc2538: Set the type of the .nrdata output section to NOLOAD

The .nrdata section is volatile, so its initialization must be controlled by the
application, and not be automatically done by the startup code. It should
neither be zeroed like .bss, nor be initialized from data in flash memory like
.data. This was already supposed to be the case, but the output section type of
.nrdata was not set to NOLOAD, causing the generated ELF .nrdata section header
to be of type PROGBITS instead of NOBITS, i.e. load data was generated to be
programmed in RAM, thus producing huge unprogrammable .bin files.

Signed-off-by: Benoît Thébaudeau <benoit.thebaudeau@advansee.com>
cc2538: Sort link input sections by alignment to optimize size

Normally, the linker does not sort files and sections matched by wildcards, so
they are placed in the order in which they are seen during link. If numerous
objects with different alignments are mixed, or if objects with unusually large
alignments are present, this very likely leads to a lot of space being wasted
because of accumulated alignment gaps.

This commit forces input sections to be sorted by alignment (unless this is
overridden by the linker script), which decreases the number and the size of
alignment gaps, thus saving space.

For a typical Contiki project, this change saves nearly 1 kiB, mainly in .bss.

Note that this behavior is only enabled if the SMALL make variable is set to 1,
because this makes more sense for a size optimization.

Signed-off-by: Benoît Thébaudeau <benoit.thebaudeau@advansee.com>
cc2538: Move SoC data to a dedicated section to save space

Some SoC data requires huge alignments. E.g., the µDMA channel control table has
to be 1024-byte aligned. This table was simply aligned to 1024 bytes in the C
code, which had the following consequences, wasting a lot of RAM:
 - As this table could be placed anywhere in .bss, there could be an alignment
   gap of up to 1023 bytes between the preceding data and this table.
 - The size of this table was also aligned to 1024 bytes, regardless of
   UDMA_CONF_MAX_CHANNEL, making this configuration option supposed to save RAM
   just useless.
 - .bss was also aligned to at least 1024 bytes, creating a huge alignment gap
   between .data and .bss.

Instead of relying on the compiler to force this alignment, and on the linker to
automatically place data, this change places carefully such SoC data in RAM
using the linker script. A dedicated section is created to place such SoC data
requiring huge alignments, and it is put at the beginning of the SRAM in order
to ensure a maximal alignment without any gap. In this way, the alignment of
.bss also remains normal, and the size of this table is not constrained by its
alignment, but only by its contents (i.e. by UDMA_CONF_MAX_CHANNEL).

In the case of the µDMA channel control table, the data is still zeroed by
udma_init() (instead of also being zeroed as part of .bss).

Signed-off-by: Benoît Thébaudeau <benoit.thebaudeau@advansee.com>
cc2538: Remove the unused vtable section

Signed-off-by: Benoît Thébaudeau <benoit.thebaudeau@advansee.com>
Fix PCAP packet header timestamp
Moved all generic IP files into the net/ip module
Moved IPv4 files into the net/ipv4 module
Moved IPv6 files into the net/ipv6 module
Updated include paths for the moved files under net/
First stab at implementing the MODULES mechanism
Use the MODULES mechanism for the native platform
Replaced the old Makefile.uip with module makefiles
Made the rime code into a separate module
Include the core/net and core/net/ip modules in the core/net/ipv4 module
Include the core/net and core/net/ip modules in the core/net/ipv6 module