Bug fixes:
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* fix handling of downstream testing when downstreams don't exist yet (e.g. bootstrapping)  #2860
* fix handling of downstream testing in tandem with --output-dir or --croot (add locations as file:// urls)  #2860
* fix improperly escaped entries in cran template.  Clean up unnecessary changes.  #2861

Contributors:
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* @mingwandroid
* @msarahan