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Adapt CLI to wdl.20260701.1 and audit findings#5

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cnluzhang wants to merge 9 commits into
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adapt-wdl.20260701.1-and-audit
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Adapt CLI to wdl.20260701.1 and audit findings#5
cnluzhang wants to merge 9 commits into
mainfrom
adapt-wdl.20260701.1-and-audit

Harden CLI diagnostics and Wrangler config handling

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