Figure asset MANIFEST

Source provenance and regeneration procedures for the foundry paper’s figure assets. Mirrors gxwf/figures/MANIFEST.md: where an asset is a generated artifact rather than a drawn diagram, the entry is a reproducible command so re-running it regenerates the asset.

Environment

• gxwf CLI: @galaxy-tool-util/cli. The draft-aware subcommands (draft-validate, draft-extract, draft-next-step) and gxwf mermaid’s draft overlay live on the draft-validate-concrete branch of galaxy-tool-util-ts (unmerged at capture date).
• Renderer-fix dependency. The step→step connectivity in these diagrams depends on the @galaxy-tool-util/schema parse fix that is currently uncommitted in the parsed_tool_fixes worktree. Pre-fix, both diagrams render under-connected (missing the staramr fan-out and the isescan → reshape chain). Regenerate only against a tree that carries that fix.
• Draft source workflows: ~/draft_workflows/MRSA/ (an MRSA antimicrobial-resistance conversion walk; not checked into this repo). step-07-mobile_reformat.gxwf.yml is the step-07 snapshot used here.

Mechanism figures (draft format)

These illustrate the draft format mechanism — what a GalaxyWorkflowDraft and its draft-extract projection look like. They are not a completed end-to-end case study and must not be captioned as Evidence-section results (see evidence.md, case-study.md). The vehicle happens to be the MRSA walk; the claim is about the format.

draft_extract — draft (planned overlay) → extracted concrete subset

Pairs with the manuscript’s “the workflow draft is the typed handoff between tiers” (Why Decomposition Works) and the draft-validate --concrete description in Methods. Two panels:

• mobile_reformat_draft.png (2753×411) — the step-07 snapshot as-is: 7 concrete steps solid/purple, 7 planned steps grey-dashed (the scaffold the per-step loop has not yet filled), mobile_reformat itself just gone solid.
• mobile_reformat_extracted.png (1205×443) — after gxwf draft-extract: the drafty steps dropped, _plan_* stripped, class promoted to GalaxyWorkflow — the clean 7-step concrete workflow that the --concrete validation stage checks against real tool schemas.

cd ~/draft_workflows
gxwf mermaid MRSA/step-07-mobile_reformat.gxwf.yml                          # → draft (planned overlay)
gxwf draft-extract MRSA/step-07-mobile_reformat.gxwf.yml -o mobile_extracted.gxwf.yml
gxwf mermaid mobile_extracted.gxwf.yml                                      # → extracted concrete subset

• Figure number / main-vs-SI placement: TBD (editorial). Distinct from Figure 5 (“the workflow draft resolves” across three tiers); this shows the extraction/projection, not the per-step resolution.
• For a deterministic repro, copy step-07-mobile_reformat.gxwf.yml (and/or the extracted output) into a capture-kit/ here once the renderer fix is committed.