Fix bug in initFile/initFileDouble isValid

* upper limits were being checked with wrong comparison
Add error checking during new step generation.
Merge branch 'base'
Change of sign of re-ordering factor (log N!)
Add ios formatting when writing chunks to streams.
Merge branch 'base'
Output acceptance fraction information
Add ability to output results to HDF5 format.

* affineChainSet::writeToHDF5 outputs the chains and likelihoods
* affineEnsemble::writeToHDF5 adds a bunch of attributes detailing
  the fit parameters, then calls affineChainSet::writeToHDF5 to
  write the chains/likelihoods.
* Add support to example programs.
Merge branch 'base'

Conflicts:
	configure.in
Add HDF5 support to P(D) fits, change like_offset

* like_offset is now based on a Gaussian model including
  the instrument noise and possibly an expected confusion noise value.
* HDF5 support in pofd_affine_mcmc