.Codex

Lock an ideation run into a single-source-of-truth brainstorm brief (`output/trace/IDEA_BRIEF.md`) and a replayable multi-query plan (`queries.md`).

Use when a broad paper candidate pool needs deterministic deduplication and a stable core set.

Write structured notes for each paper in the core set into `papers/paper_notes.jsonl` (summary/method/results/limitations).

Extract per-subsection “anchor facts” (NO PROSE) from evidence packs so the writer is forced to include concrete numbers/benchmarks/limitations instead of generic summaries.

Retrieve arXiv paper metadata with keyword queries or import an offline arXiv export, and save results as JSONL (`papers/papers_raw.jsonl`).

Write `output/DRAFT.md` (or `output/SNAPSHOT.md`) from an approved outline and evidence packs, using only verified citation keys from `citations/ref.bib`.

Fill `outline/tables_index.md` from `outline/table_schema.md` + evidence packs (NO PROSE in cells; citation-backed rows).

Instantiate or update a workspace `UNITS.csv` from a selected pipeline and units template (deps/checkpoints/acceptance).

Use when `evidence-review` has an extraction table and needs lightweight risk-of-bias fields.

Use when an approved tutorial spec exists and the run needs a deterministic prerequisite graph before module planning.

Screen the direction pool with a discussion-first scoring pass, writing `output/trace/IDEA_SCREENING_TABLE.md`.

Use when `paper-review` has claims plus evidence gaps and needs the final referee-style report.

Fetch and normalize supported source-tutorial inputs into local, traceable text artifacts.

Execute exactly one eligible Unit in an existing research Workspace; use for stepwise or manual semantic execution when status, Attempt, Artifact, Manifest, checkpoint, and acceptance evidence must remain synchronized.

Build per-chapter (H2) writing briefs (NO PROSE) so the final survey reads like a paper (chapter leads + cross-H3 coherence) without inflating the ToC.

Audit-style editing pass for `output/DRAFT.md`: remove template boilerplate, improve coherence, and enforce citation anchoring.

Create per-subsection evidence packs (NO PROSE): claim candidates, concrete comparisons, evaluation protocol, limitations, plus citation-backed evidence snippets with provenance.

Write one survey-quality paragraph from evidence packs (tension → contrast → evaluation anchor → limitation).

Scaffold a LaTeX project (`latex/main.tex`, optional bibliography wiring, structure) from an existing Markdown draft.

Use when a tutorial concept DAG exists and the run needs an ordered teaching plan with objectives and outputs.

Use when `paper-review` needs overlap/delta positioning against provided related work.

Build chapter-level briefs (`outline/section_briefs.jsonl`) from chapter skeleton plus section bindings before stable H3 decomposition.

Map papers from the core set to each outline subsection and write `outline/mapping.tsv` with coverage tracking.

Deterministically merge the final fingerprinted section snapshot into `output/DRAFT.md`, preserving outline order and inserting transitions only when explicitly enabled.

Draft non-prose visuals artifacts (timeline, figure specs) for a survey, grounded in evidence and using citation keys from `citations/ref.bib`.

Initialize a missing research Workspace from the repository template without overwriting existing Run state; use before Pipeline binding when the target under `workspaces/` has no valid core artifacts.

Generate a Beamer slide deck from the final tutorial and approved module structure.

Bind addressable evidence IDs from `papers/evidence_bank.jsonl` to each subsection (H3), producing `outline/evidence_bindings.jsonl`.

Use when `evidence-review` has screened includes and needs a schema-aligned extraction table.

Global consistency review for survey drafts: terminology, cross-section coherence, and scope/citation hygiene.

Rewrite subsection openers so they stop reading like a generated table-of-contents: remove \"overview/narration\" stems and reduce repeated opener cadences across H3s.

Convert a taxonomy (`outline/taxonomy.yml`) into a bullet-only outline (`outline/outline.yml`) with sections/subsections.

Planner-pass coverage + redundancy report for an outline+mapping, producing `outline/coverage_report.md` and `outline/outline_state.jsonl`.

Route an unbound research Goal to one Workflow or materialize its initial C0 kickoff block; use during initial binding, not for later checkpoint summaries or approval.

Use when `evidence-review` needs an operational protocol before screening and extraction.

Use when a `research-brief` workspace has a small paper set plus outline and needs a compact reader-facing briefing instead of a full survey.

Build or validate the source manifest for the source-tutorial pipeline from user-provided URLs/files.

Writing self-loop for surveys: run the strict section-quality gate, then rewrite only the failing `sections/*.md` files until the report is PASS.

Build a retrieval-informed chapter skeleton (`outline/chapter_skeleton.yml`) from taxonomy/core scope before stable H3 decomposition.

Project completed stage Artifacts into a concise human-review block in `DECISIONS.md`; use before a Workflow checkpoint, not for Workflow routing or approval.

Use when a review workspace has manuscript text and needs a traceable claim ledger.

Use when `paper-review` needs a claim-by-claim evidence gap report grounded in an extracted claim ledger.

Use when a tutorial module plan exists but each module still needs a verifiable teaching loop.

Review and record one pending human checkpoint in a research Workspace; use when a HUMAN Unit is blocked on an `Approve C*` decision, and never treat silence or artifact existence as approval.

Synthesize the shortlist into a discussion-ready research idea brainstorm memo, writing `output/REPORT.md`, `output/APPENDIX.md`, and `output/REPORT.json`.

Compile a LaTeX project and run basic QA (missing refs, bib errors, broken citations), producing `latex/main.pdf` and a build report.

Merge/simplify an over-fragmented outline to hit a paper-like section budget (NO PROSE): target final ToC ~6–8 H2, fewer thicker H3.

Audit/regression checks for the evidence-first survey pipeline: citation health, per-section coverage, placeholder leakage, and template repetition.

Bind papers to chapter-level sections first, writing `outline/section_bindings.jsonl` and `outline/section_binding_report.md`.

De-slot and harmonize paper voice across `sections/*.md` without changing meaning or citation keys.

Use when `evidence-review` has completed extraction and needs a bounded narrative synthesis.

Build a 2+ level taxonomy (`outline/taxonomy.yml`) from a core paper set and scope constraints, with short descriptions per node.

Build a final, machine-readable argument snapshot from current H3 sections and refresh section fingerprints before merge.

Compile the Beamer tutorial deck and write a build report.

APPLIES/consumes a `citation-diversifier` budget report (`output/CITATION_BUDGET_REPORT.md`) to inject *in-scope* citations into an existing draft (NO NEW FACTS), so the run passes the global unique-citation gate without citation dumps.

Generate and verify BibTeX entries from paper notes, writing `citations/ref.bib` and `citations/verified.jsonl`.

Evidence self-loop for surveys: read evidence bindings + evidence packs, then write an actionable upstream TODO plan (which stage/skill to fix) before writing more prose.

Expand and refine search keywords (synonyms, acronyms, exclusions) and update `queries.md`.

Rewrite limitation passages so the paper keeps limitations without falling into count-based slot phrases (e.g., \"Two limitations…\") across many H3s.

Use when `paper-review` needs a canonical manuscript text artifact before claim extraction.