Evidence

Current evidence snapshot for manuscript.md. The manuscript now treats notebook-driven extraction, report continuity, and external-agent notebook authorship as delivered behavior, not as an evaluation plan.

Delivered System

• History-attached Pages via Page.history_id.
• Revision provenance via PageRevision.edit_source.
• Page-scoped chat via ChatExchange.page_id.
• History-aware notebook assistant tools.
• Shared editor, diff, revision, rendering, and API paths for notebooks and standalone reports.
• MCP notebook operations for external-agent authoring, with agent edits recorded as edit_source="agent" and restores as edit_source="restore".

Vignette Evidence

• Vignette 1: mobile resistome. Four-isolate S. aureus ARG-to-insertion-sequence context analysis. Notebook-referenced on-graph tables and heatmaps extract to a 14-step, 9-output, sample-agnostic workflow that re-runs byte-identical to the validated original.
• Vignette 2: differential ATAC-seq. Corces 2016 hematopoiesis count-matrix analysis contrasting erythroblast and B-cell accessibility. Notebook-referenced PCA, volcano, significant-peak, and ranked top-gained outputs extract to a 13-step, 6-output workflow that reproduces the 45,620 significant-peak result and lineage master-regulator loci.
• Vignette 3: differential ChIP. TAL1 G1E-versus-megakaryocyte binding analysis. A single extraction reproduces the analysis but is condition-pinned; reusable decomposition yields a 5-step map-over peak caller and 29-step pairwise comparator.

Evidence Layers

• Implementation completeness: migrations, API, frontend, assistant tools, revision behavior, MCP operations, and test coverage.
• Worked notebook artifacts: Figures 1-3 show notebooks with on-graph outputs, not pasted figures.
• Workflow handoff: Table 1 and SI Workflows S1-S5 show extracted workflow structure, clean inputs, exposed outputs, and re-run behavior.
• Agent authorship: Figure 4 shows MCP-authored revisions recorded as agent-authored notebook revisions.

Remaining Evidence Gaps

• Exact Galaxy PR number(s), commit range, and release target.
• Current test counts by layer.
• Final venue-specific availability/data-availability handles.
• Optional report-continuity screenshot showing notebook narrative inside an extracted workflow report.