Argument handling fix.
Fixed warnings when running MakeDocs.PL.
Added version control content to 'Getting started' section of manual, added 'Putting it all together' section with guidance on tuning PMMH.
Merge branch 'master' of https://github.com/lawmurray/LibBi
Reviewed new sections of manual. Added tip on simulating a data set.
Added tip to manual on using ncdump.
Fixed sampling of joint distribution, '--target joint' should imply
'--with-param-to-state'.
Updated version to 1.0.1.