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v1-residue-sweep

v1-residue sweep: find every v1/KRAS reference across the project

Metadata

Statusdone
Assignedagent-30
Agent identity3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3
Created2026-05-01T18:39:15.309972074+00:00
Started2026-05-01T18:40:07.719859823+00:00
Completed2026-05-01T18:48:14.886630906+00:00
Tagsgrant,urgent,v2-pivot, eval-scheduled
Eval score0.82
└ blocking impact0.93
└ completeness0.85
└ constraint fidelity0.85
└ coordination overhead0.90
└ correctness0.80
└ downstream usability0.82
└ efficiency0.85
└ intent fidelity0.90
└ style adherence0.88

Description

Description

The v2 pivot (2026-04-24) replaced the KRAS cancer spine with PHR discovery in pangenomes. The Google.org submission is due TODAY. The risk: v1 framing surviving in any artifact a reviewer or visitor could see while the v2 application is being evaluated.

The submission-readiness-audit task is already auditing workgraph_google_application_FINAL_v2.md itself. This task is the COMPANION sweep — everywhere ELSE.

What to do

Grep the entire repo and any tracked sibling artifacts for v1-spine terms. Flag every hit with file path + line number + recommended action (delete / rewrite / archive / leave-with-note).

Search terms (case-insensitive)

  • KRAS, KRAS G12D, G12D
  • MRTX1133
  • pancreatic cancer, pancreatic, oncology, tumor
  • Boltz, RFdiffusion, RFDiffusion, DiffDock
  • 'drug discovery competition', 'deep research competition' (the v1 demo framing)
  • 'wrote this proposal with WorkGraph', 'drafted using WorkGraph', 'incorporated using WorkGraph' (the cut recursion claim)
  • 'CRISPRme provided off-target analysis for the BCL11A guide used in Casgevy' (and close paraphrases — the inaccurate Casgevy framing)
  • 'PI' / 'lead PI' (style rule violation, often correlates with old text)

Where to look

  • Top-level: workgraph_extended_outline.md (v1 — should exist but not be cited from canonical paths)
  • Top-level: workgraph_google_application_FINAL.md (v1)
  • Canonical v2 docs: workgraph_extended_outline_v2.md, STATE.md, README*.md, CLAUDE.md
  • Landing page: index.html, website/index.html — CLAUDE.md flags 'What we've built' card #3 specifically
  • .wg/ notes and any tracking docs
  • Any other markdown / html in the tree

Classification of each hit

  • OK (historical context) — explicit acknowledgment that the item is v1/superseded (e.g. STATE.md §5 decision log, CLAUDE.md 'Superseded' section). Leave alone.
  • MUST REMOVE BEFORE PUBLIC TRAFFIC — anything a Google.org reviewer or website visitor could land on that still presents v1 as current. Top of list: landing page card #3.
  • PUBLIC REPO HYGIENE — poietic-pbc/deep-research-competition (public, stale). Recommend: archive the repo OR add a top-of-README banner pointing to v2 PHR demo. Do not delete (loss of git history).
  • CAN WAIT — internal-only files where v1 references won't be seen by reviewers in the next 24h.

Output

Write .wg/v1-residue-sweep-20260501.md with sections matching the four classifications above. For each MUST REMOVE item, include the exact replacement text or 'delete this block'. wg log a one-line summary (e.g. 'N must-fix, M public-hygiene, K can-wait').

Validation

  • Every search term grepped across repo
  • Landing page card #3 explicitly checked
  • poietic-pbc/deep-research-competition repo status noted
  • Each hit classified into one of the four buckets
  • MUST REMOVE items have concrete fix text, not just a flag
  • Output file written to .wg/v1-residue-sweep-YYYYMMDD.md

Depends on

Required by

Log