Resurrect iteration over measurements in report gen

Makes report generation respect n_recent_meas in the yaml file, which it used to do before some changes caused this to break. Addresses #186.

Along the way, fixes a tiny bug with exception handling in _util.py, and creates an option for the report yaml to override the default output directory (used while developing to keep results out of a shared folder, figured it would be handy for investigations later too).

Large blocks of changes are just the result of indentation, bringing them back into the loop that previously existed.