Add --short-output flags to hide log messages about what isn't needed #430
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I've added a flag to make the output easier to read when a run is already partially complete. The flag
--short-output
supresses any log messages about steps that have already completed. This also involved converting the non-package scripts into acting like packages. The names of a package are only supressed if the package would be skipped entirely (through use of --no-extras), if the package just doesn't after any steps to run then the name is still shown but none of the steps under it are shown.