Only check configuration/schemas/versions in output repositories

When running CmdLineTasks, we check that the configuration, software versions, and catalog schemas used are consistent with those used in any input/output repositories. This is frequently not the behavior we want: we often want the new processing to explicitly differ from the input repositories because they're going into a new output repository. To achieve this, users often have to specify the --clobber-config and --no-versions options.

With the changes in process on DM-12450, it will be possible to check only that the configuration, software versions, and catalog schemas are consistent with those in the output repositories, making the use of --clobber-config and --no-versions much less frequent.