Changes to handling of run number
 -- May now be specified in the command line (--run or -r)
 -- New option run-min-digits to padd smaller run numbers with zero
    (default 5 digits)
 -- Clean up RunAction and Analyzer. Run action no longer keeps local
    copy of run number, or auto save integer. It didn't use them before
    besides just passing them onto the analyzer.
 -- Analyzer now has SetRunNumber, SetRunMinDigits, and SetAutoSave
    functions