Remove errant logging message about chain number

Rely on stan::common for this kind of reporting.
Fix argument handling for HMC
Fix corner case when calculating number of digits in summary
Report chain number in progress
Really fix bug where pip -e would not run install_clib

Hopefully closes a long-standing bug where one could not install from source
with ``pip install -e .``

This change was previously reverted. Hopefully this version will last.