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Refactor package and download software

Matthew Kenigsberg requested to merge mkenigs/pipeline-definition:prepared-software into main

Currently, code to package and download software is mixed together, and it detects which operation is needed. This change cleanly separates the packaging and downloading code, only running the packaging code in prepare, and downloading software in every other stage

Depends !1304 (merged) and !1305 (merged)

Edited by Matthew Kenigsberg

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