Make optimization opt-in by default & update docs

This will probably change in the future, when the optimization algorithms
implemented are a little more robust.  Also, maximization of the posterior pdf
is not automatic.
Remove old method call
Seed with MAP estimator where necessary
Merge pull request #282 from dmcdougall/minimize-opt-in

Make optimization opt-in by default
Fix for cobra test for VPATH builds
Clean up turds during a make distclean
Remove trailing whitespace
Merge pull request #293 from pbauman/vpath-fixes

Fix for cobra test for VPATH builds
Merge pull request #294 from dmcdougall/more-vpath-fixes

More vpath fixes
Add compactly supported transition kernel
Implement new transition kernel for bounded domains
Add joint pdf docs for invlogitgaussian
Add docs for invlogitgaussianvectorrv
Add docs for InvLogitVectorRealizer
Add docs for the new TK
Fix some bugs in the invlogit distribution

1. Deal with the pdf at the boundary better
2. Fix a bug where the wrong transform was being taken for left-open domains
Update regression tests with new reference solns

We need to do this because the transition kernal as changed for DRAM and so
different samples are drawn.
Update ignores.  It's bad these keep piling up
Fix a comment
Update changelog