Cli: Make sure that ChangeLog directory exists on 'repository commit'

refs #7255
Cli: Don't overwrite existing objects; delete old agent objects on 'agent update-config'

refs #7248
Cli: Bail early on 'repository commit' if changelog dir does not exist

refs #7255
Cli: Add agents.conf w/ default agent templates for 'agent update-config'

refs #7248