praefect: Don't overwrite '-older-than' flag

Currently the list-untracked-repositories subcommand fails to honor the value passed in the -older-than flag. This is due to our calling cmd.FlagSet() again after args have been parsed, resetting cmd.onlyIncludeOlderThan back to its default value.

Resolve this by getting the subcommand name from the already parsed flags passed in.

Fixes #4294 (closed)