Allow setting default values in the model

... and use it for tolerance, leap_min_jump, and InjecitionStim.end.
Remove a bunch of useless methods
ResultWriterHDF5: write results in much bigger chunks

When running multiple writers, writing small pieces of data
was the main bottleneck. Work around this by slowly filling
an array and writing it out in one chunk.
NextEventQueue: be smarter when checking if propensity was updated properly

Before, the old population and the new population were compared, and if
the it was different but the propensity didn't change, an exception was thrown.
This check is crucial, because if the propensity is recalculated without chaning,
we can assume that the propensity update algorithm isn't working properly.
But with multiple substrates, if one goes up, and the other down, propensity
might remain constant. Check this explicitly, by comparing arrays of old
and new populations in the slow path.
Extract the trial-independent part of calculations from BaseCalc

When running multiple trials in parallel, those calculations were needlessly
repeated, and because those calculations actually update the state of the
source objects, they weren't idempotent. Fix both problems by doing them
before any parallel calculations start.
VolumeGrid: simplification
anim_concentrations: update to new layout, but only for trial0 for now
Allow setting the number of threads with stochdiff.threads=<n>
Improve debugging messages
ResultWriterHDF5: fix off-by-one in array filling

Basically, the array was written one event to late.
NextEventQueue: fix (again) the calculation of stimulation leap times

Previous version was just buggy, and was failing with Asia's model.
HDF5ResultWriter: write simulation seed
Allow overwriting of sdrun settings on the command line

"-Dstochdiff.sdrun.runtime=200" etc.
ExactStochastic: log the simulation runtime and simulation speed

The time and speed ignore the initial setup time, so they are meaningful
for short runtimes even with big models where the setup if fairly expensive.
fixup! Allow overwriting of sdrun settings on the command line
Rework the writing of events one more time

It seems that
a) using large chunksize is not beneficial
b) interleaving getData() with other operations leads to corruption and slowdown
c) the first row in each extensible array had bogus results since always

With current changes, the slowdown from one writer is on the order or single percent,
and with 8 writers it is on the order or 10-20%, which should be tolerable for now.
Improve logged messages a bit
Always call the simulation seed so

becausing calling it calculation seed in places was just confusing.
anim_concentrations: add --trial option
Make sure that we write results at the very end