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Diamond: fix align/unaligned output #6262

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FOR CONTRIBUTOR:

  • I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • License permits unrestricted use (educational + commercial)
  • This PR adds a new tool or tool collection
  • This PR updates an existing tool or tool collection
  • This PR does something else (explain below)

Fixes #6170 hopefully

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Diamond: optional outputs produced do not respect tool form settings
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