Implement Roland Brochards' new acceleration maths clock-based.

His implementation was done on every step and as it turns out,
the very same maths works just fine in the clock interrupt.
Reason for the clock interrupt is: it allows about 3 times
higher step rates.

This strategy is not only substantially faster, but also
a bit smaller.

One funny anecdote: the acceleration initialisation value, C0,
was taken from elsewhere in the code as-is. Still it had to be
adjusted by a factor of sqrt(2) to now(!) match the physics
formulas and to get ramps reasonably matching the prediction
(and my pocket calculator). Apparently the code before
accumulated enough rounding errors to compensate for the
wrong formula.
Fix endstop stop condition for clock-based acceleration.

This required a strategy change, since move_state.n is no longer
decreasing in steps of 1.
dda.c/.h: move n and c back into the dda structure.

This is a preparation for starting a move from non-zero speeds,
which is needed for look-ahead. Keeping both variables in
move_state and doing the calculations in dda_start() is possible
in principle, but might not fit the tight time budget we have when
going from one movement to the next at high step rates.

To deal with this, we have to pre-calculate n and c, so we have
to move it back into the DDA structure. It was there a year ago
already, but moved into move_state to save RAM (move_state exists
only once, dda as often as there are movement queue entries).
dda.c: re-gain look-ahead compatibility.

We're here! Incredible high step rates as well as smooth
movements due to look-ahead.
look-ahead: take F_start into account on acceleration calculations.
look-ahead: take F_end into account on acceleration calculations.
dda.c: simplify start conditions calculation.
Restore simulation build target.

This code was accidentally removed long ago in a botched merge. This
patch recovers it and makes it build again. I've done minimal testing
and some necessary cleanup. It compiles and runs, but it probably still
has a few dust bunnies here and there.

I added registers and pin definitions to simulator.h and
simulator/simulator.c which I needed to match my Gen7-based config.
Other configs or non-AVR ports will need to define more or different
registers. Some registers are 16-bits, some are 8-bit, and some are just
constant values (enums). A more clever solution would read in the
chip-specific header and produce saner definitions which covered all
GPIOs. But this commit just takes the quick and easy path to support my
own hardware.

Most of this code originated in these commits:

	commit cbf41dd4adbdac8bd1ce0288b94266342fb62609
	Author: Stephan Walter <stephan@walter.name>
	Date:   Mon Oct 18 20:28:08 2010 +0200

	    document simulation

	commit 3028b297f31fa805db4c6f5077e1c3edb0ca5099
	Author: Stephan Walter <stephan@walter.name>
	Date:   Mon Oct 18 20:15:59 2010 +0200

	    Add simulation code: use "make sim"

Additional tweaks:

Revert va_args processing for AVR, but keep 'int' generalization
for simulation. gcc wasn't lying. The sim really aborts without this.

Remove delay(us) from simulator (obsolete).

Improve the README.sim to demonstrate working pronterface connection
to sim. Also fix the build instructions.

Appease all stock configs.

Stub out intercom and shush usb_serial when building simulator.

Pretend to be all chip-types for config appeasement.

Replace sim_timer with AVR-simulator timer:

The original sim_timer and sim_clock provided direct replacements
for timer/clock.c in the main code. But when the main code changed,
simcode did not. The main clock.c was dropped and merged into timer.c.
Also, the timer.c now has movement calculation code in it in some
cases (ACCELERATION_TEMPORAL) and it would be wrong to teach the
simulator to do the same thing. Instead, teach the simulator to
emulate the AVR Timer1 functionality, reacting to values written to
OCR1A and OCR1B timer comparison registers.

Whenever OCR1A/B are changed, the sim_setTimer function needs to be
called. It is called automatically after a timer event, so changes
within the timer ISRs do not need to bother with this.

A C++ class could make this requirement go away by noticing the
assignment. On the other hand, a chip-agnostic timer.c would help
make the main code more portable. The latter cleanup is probably
better for us in the long run.
Move argc/argv processing deeper into simulator.

Less magic == more better.
Add debug pin-tracing code for investigation.
WIP: Add simulator data-logging.

Record simulation run-time data in file 'datalog.out' so it
can be analyzed after-the-fact or during the run.

This feature is evolving. Eventually it should be compatible with
some logic analyzer GUIs such as gtkwave or even gnuplot.
simulator: fix timer overflow problem

Next-interrupt-time calculations were made in 16-bit registers but
moved to 32-bit ones for convenience.  But they forgot to round off
at 16-bits.  Force the round-off so we do not wait forever.
Split Makefile-SIM out from Makefile-AVR.

Also, some makefile cleanup:

 - Remove obsolete 'depend' target.
 - Move AVR-specific targets to AVR makefile.
 - Add TARGET variable to identify target to make and to clean.
 - Tidy up dependency make.
Makefiles: auto-dependencies cleanup.

Dependency automation seems a bit confused in these makefiles.
Clean it up following ancient sage wisdom here:
http://mad-scientist.net/make/autodep.html

In short, use -MMD to generate dependency files for each .o target,
and then use a sed script to extend that to avoiding "missing file"
dependencies when headers are renamed/removed.

Also, make everything dependent on makefiles other than our
autodependency (*.P) makefiles.

Make the BUILDDIR an order-only prerequisite for our targets so any
changed file therein does not cause all other files to appear to be
out of date.
dda.c: re-enable the hack with overly large rampup steps.

Until we have accurate rampup steps calculations, this hack is
neccessary for endstop searches.
dda.c: deal with endstop hits while still accelerating.

Also, move_state.step_no must be read atomically.
gcode_process.c: show endstop status in clear text.

This costs 40 bytes, but should be a significant enhancement on
usability.
Simulator cleanup
simulator: Add nano-timer to datalog
simulator: record g-codes in datalog

Add comment stream to datalog output so we can store g-codes and
other events that occur during simulation.