Add 'Workflows in the AI era' side quest#679

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pinin4fjords wants to merge 12 commits into

workflow-management-fundamentals-side-quest-v2

Commits on Apr 30, 2026

Restructure: place side quest at workflows_in_the_ai_era/

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Migrate scripts to workflow output system, drop meta maps

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Rewrite as 'Workflows in the AI era' with AI framing throughout

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Tweak nextflow.config: --platform=amd64 and drop report blocks

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Fix hl_lines counts; tidy takeaway labels; rename README

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Reorder install + tighten 3.1.3 from /run-tutorial walkthrough

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Make AI-era framing symmetric: agent writes both forms

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Restructure narrative around 'the artefact must outlive the conversation'

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Trim intro to ~150 words, let section 2 do the artefact work

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Make AI thread structural in Parts 1 and 2, not garnish

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Address review: MULTIQC in solution, doc/solution alignment, hl_lines

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Address pr-679-review.md from second-AI review pass

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