(MCO-265) - Deprecate the #run method

This commit adds a deprecation warning to the run method. After warning
the run method will call main_loop, the method that replaced it.
(MCO-265) Update mcollectived to use main_loop everywhere

This commit fixes mcollectived to use the main_loop method instead of
run everywhere.
Merge pull request #182 from ploubser/improvement/master/mco-0265

MCO-265 Deprecate run method in runner and update mcollectived to use main_loop everywhere