Fix bug in data file reading, simplified error # scheme for specfile.

* exp_conf was being passed as histogram log step in calcLike file reads.
* Added specFile/specFileDouble hist_logstep= option to set histogram
  log step.
* Simplify error message numbering scheme for specFile/specFileDouble::readFile
Use affineExcept in beam::readFile errors rather than just std::cerr.
Add exp_conf support to pofd_affine_getLike
Change name 'sigma knots' for initFiles to range, other minor changes.
Add option to have initial steps taken at a higher temperature.
Merge branch 'base'
Initial temperature changes.
Change the way the maximum R flux is handled.

* In both calcLike and calcLikeDouble, rather than using
  the maximum data flux, the larger of either the maximum
  data flux or the maximum model flux is used.
* Changed the flux safety to 1.1 from 1.2 since in most
  cases we are now going out further anyways because of the
  previous bullet point.
Some tweaks to the maximum flux calculated.

* Tweaks to maxflux
* Avoid re-zeroing already 0 r values for padding.
Added mechanism for rejecting parameters in getLogLike

* getLogLike can now signal invalid params using a second argument.
  This automatically rejects the step.  The idea is that sometimes
  it's hard to know a parameter set is invalid without some complicated
  piece of computation only available to the likelihood computation.
* Make sure at least some steps are accepted during initial step set
  or burn in as a guard against some mistake causing all steps to
  be rejected by the above.
* This does mean it is important for the initial state to have
  actual likelihoods available.  If not, it's possible the first
  step will be rejected as invalid, and then the initial step to
  be propogated along in a way that skipFirstStep can't handle.
Merge branch 'base' into topknot
Handle invalid parameters (wrapping issues) for P(D) likelihood.
Add helper for computing log-likelihoods of most recent steps.

The idea is that it may be convenient, for expensive likelihood
calculations, to initialize the params without setting the likelihoods,
but then it's nice to be able to actually fill them in.

* Added ability to replace most recent step (replaceLastStep) in
  affineStepChunk and affineChainSet.
* Added calcLastLikeLikelihood to affineEnsemble to compute
  the most recent step likelihood in parallel.
* sample and doSteps now call calcLastLikelihood at the beginning
  to make sure they have valid likelihoods.
* A consequence of the above is that the initial position must be
  valid or the code throws an exception and crashes.
* Add test of replaceLastStep to chain_test
* Bump version number to 0.2.4.
Merge branch 'base' into topknot

Conflicts:
	configure.in