orchestrate-paper

name

orchestrate-paper

description

Goal-driven conductor for the whole idea-to-published-paper lifecycle. Takes a research idea plus experiments and a target ("submit to NeurIPS 2026", or "help me pick a venue") and runs a goal->plan->execute->verify->reflect loop. It plans the stages, invokes the right lifecycle skills in order (literature-review, write-abstract, preflight-check, simulate-reviewers, and the rest), checkpoints with the author before each stage, and re-verifies the live CFP via parse-cfp rather than trusting a cached profile. Use when a researcher says "take my idea to a submitted paper", "run the whole pipeline", "orchestrate the paper for venue X", "what's the plan from here", or "what's done and what's next". Copilot, not autonomous author. It stops to ask at every stage gate, never fabricates results or citations, and never submits. Trigger words - orchestrate, pipeline, end to end, whole paper, idea to submission.

Orchestrate Paper

The conductor. The author brings a technical idea, their experiments, and a target — a venue, or "help me pick one." This skill sets the goal ("submission-ready for venue X by deadline D") and runs a goal → plan → execute → verify → reflect loop across the whole lifecycle: it plans which sub-skills run and in what order, invokes them, checkpoints with the author at every stage gate, and uses external, measurable signals — not its own say-so — to confirm each stage actually moved the paper forward before going on.

It does not write the paper for the author and it never submits anything. It coordinates the specialists (each of which is its own skill) and keeps a durable, reviewable record in paper-workspace/ so the author can pause, inspect, reject, and resume at any point.

This skill follows a few non-negotiable working principles at every checkpoint: name assumptions, show competing readings, surface tradeoffs, stop when confused, verify live, and keep the author the author.

When to use

• "Take my idea + results to a submission-ready paper for VENUE." / "Run the whole pipeline." / "Be my copilot from idea to submission."
• "What's the plan from here?" / "What's done, what's next, what's blocking me?"
• Mid-cycle coordination: "I just got reviews back — what now?" or "we were accepted; drive camera-ready + artifacts."
• The author has many skills available and wants one entry point that sequences them instead of running ~20 by hand.

When NOT to use

• A single, well-scoped task ("polish this paragraph", "check my citations"). Call that one skill directly — the orchestration overhead isn't worth it.
• The author wants the text written for them with no review. That is not what this is; it is a copilot, and the author authors.

Inputs

1. The idea + experiments — what the paper claims and the evidence the author already has. The orchestrator never invents results to fill gaps; a missing experiment is surfaced as a blocker, not fabricated.
2. The target — a venue+track, or help me pick (routes through select-venue first). Either way, the live CFP is re-verified, never trusted from a cached profile.
3. Whatever draft exists — from a blank idea to a near-final .tex. The plan adapts to the current state (see the state script below).
4. .paper-memory/ — positioning (profile.yml), accumulated lessons.md, and decisions.md following the paper-memory-convention.md pattern. Read at start.

The loop

For the full stage → skill → exit-criterion → checkpoint-question table, read references/pipeline-map.md. The loop per stage:

1. GOAL. State the goal in one sentence and the current target (venue+track+deadline). If the target is unset, run select-venue, record the choice in .paper-memory/decisions.md, and confirm with the author before treating it as fixed (principle #1, #6).

2. PLAN. Produce a reviewable, up-front plan — which sub-skills will run, in what order, and why — from the pipeline map, adapted to the draft's current state. Plan-then-execute beats reactive step-by-step here: the author gets a roadmap to approve. Show it; do not start executing a multi-stage plan silently.

3. EXECUTE. Run the stage's sub-skill(s). Each writes its artifact to the right paper-workspace/<stage>/ folder and appends to INDEX.md. The orchestrator does not re-implement a specialist; it invokes it.

4. VERIFY — on external signals, never self-judgment. Confirm the stage met its exit criterion using a measurable check, because a model's self-reflection validates its own hallucinations (see references/verification-signals.md). Signals are concrete: latexmk/compile exit code, page count vs the live venue limit, anonymization linter, a BibTeX entry resolving to a real DOI via verify-citations, a claim tracing to a real result via verify-claims, the reported numbers reproducing from the artifact via verify-results, a checklist-presence grep, a script's pass/fail. If no external oracle exists for a step (a judgment call), say so and escalate to the author rather than letting the model grade itself.

5. REFLECT — did it measurably improve? Run reflect-and-improve against the stage goal and the before/after measurable target. Accept the stage only if the signal improved (or held while another did). Never accept a change that lowers a measurable score. Respect stop conditions (below) so the loop can't spin.

6. CHECKPOINT. Present at the stage gate: what was done, the tradeoffs, the competing interpretations where they exist, and the one checkpoint question from the pipeline map. Wait for author sign-off before the next stage. This is the durable pause point — state is on disk, so the author can leave and resume.

Run the state script at any time to see where things stand:

python3 scripts/pipeline_state.py status --workspace paper-workspace

It reads paper-workspace/INDEX.md (and an optional pipeline-state.json) and prints what's done / what's next / blocked-on plus the current goal and the pending checkpoint. Other subcommands: init, set-goal, next, advance, block, checkpoint, and signoff (the author clears a raised checkpoint so the loop can advance). Run python3 scripts/pipeline_state.py --help.

Worked example (one loop, end to end)

Author: "Take my idea + results to a submission-ready paper for NeurIPS 2026."

# GOAL — record the target and open the durable log
python3 scripts/pipeline_state.py init --workspace paper-workspace
python3 scripts/pipeline_state.py set-goal --workspace paper-workspace \
    --goal "submission-ready for NeurIPS 2026 main track" \
    --venue "NeurIPS 2026" --track main --deadline "2026-05-15 AoE"

Lock requirements first (hard stop). Before planning, run parse-cfp on the live CFP — never the cached venues/conferences/neurips-2026.yml. Suppose it returns a 9-page limit and double-blind review, each carrying a source URL + the date fetched. Raise the checkpoint and wait:

python3 scripts/pipeline_state.py checkpoint --workspace paper-workspace \
    --stage parse-cfp \
    --question "9pp, double-blind, NeurIPS checklist required, AoE deadline — confirm before we build on these?"

The author confirms. Now PLAN: show the stage list from the pipeline map adapted to the draft's state (a half-written .tex, no related work yet), get approval, then EXECUTE one stage — say preflight-check. VERIFY on an external signal, not the model's say-so: check_sections.py exits 0 and the PDF is 9 pages against the 9-page live limit. REFLECT: the desk-reject count went 2 → 0, an improvement, so accept. Record it and raise the next checkpoint:

python3 scripts/pipeline_state.py advance --workspace paper-workspace \
    --stage preflight-check --signal "check_sections.py exit 0; 9pp <= 9 live limit; anonymizer clean"
python3 scripts/pipeline_state.py status --workspace paper-workspace   # done / next / blocked

If a later stage exposes a gap — e.g. simulate-reviewers predicts R2 will ask for an ablation the author doesn't have — that is a blocker, not something to fabricate: block --stage simulate-reviewers --on "missing ablation R2 will ask for", surface it, and let the author decide. Submission is never the orchestrator's action: it hands over a ready package and stops.

Stop conditions (so the loop can't spin forever)

Configurable, but always present — the loop must terminate:

• Stage exit met — the measurable criterion in the pipeline map passes.
• Diminishing returns — a reflect pass improves the metric by less than a small delta (e.g. prose-lint delta < N); stop polishing.
• Hard iteration cap — at most ~3 refine passes per stage, then escalate.
• Budget cap — stop and report when a token/time budget is hit.
• Escalate to author — when an unverified assumption gates the next step, the request has more than one reading, or the model is genuinely confused (principles #1, #2, #4). Escalation is a first-class outcome, not a failure.

Live verification is mandatory

Venue rules change every cycle and the model's memory of them is stale by construction. Before any stage relies on a deadline, page limit, blinding level, template, checklist, or artifact-badge rule, re-fetch it from the live CFP via parse-cfp and prefer that over any venues/conferences/*.yml cached profile. Every venue fact the orchestrator carries into a checkpoint must keep its source URL and the date it was fetched, so the author can click through and confirm. Overconfidence is highest right after a fetch, so re-check the fetched fact against the primary source before acting on it. Never hardcode a venue rule into this skill.

Output

• A running plan + per-stage artifacts under paper-workspace/, each logged in INDEX.md — the durable, reviewable record.
• A live what's-done / what's-next / blocked-on view from pipeline_state.py.
• A short narrative at each checkpoint: done, tradeoffs, the decision the author needs to make. Never a draft presented as finished-and-submitted.

Adapt to your discipline

The pipeline map includes common conference and journal rails. Fork it: reorder stages for a journal (revise-and-resubmit instead of rebuttal), swap citation norms, and adjust which checklists, ethics statements, data policies, or artifact tracks apply in your field. Keep the stage gates; change what runs inside them.

Guardrails

• Copilot, never pilot. It plans and coordinates; it never fabricates results or citations, never claims acceptance or predicts a decision, and never submits to any system on the author's behalf.
• Verify on external signals, not self-reflection. The completion signal is always a compile/lint/DOI-resolve/checklist/human-sign-off — never the model grading its own output (see references/verification-signals.md).
• Stop at every stage gate. Author sign-off is required between stages; high- stakes transitions (treating a CFP card as ground truth, sending a rebuttal, camera-ready) are hard stops.
• Durable checkpoints. Persist each stage artifact + INDEX.md before advancing, so a pause/restart never re-runs prior skills (avoiding duplicate API calls against the key-free search stack).
• Don't double-deadline. Track the artifact-evaluation / camera-ready track as a separate post-acceptance deadline, not folded into the paper deadline.
• One file under 500 lines; references/ one level deep; scripts stdlib-only with --help and clean nonzero exits.

Memory

Uses the shared .paper-memory/ convention described by paper-memory-convention.md.

• At start: read profile.yml (positioning), lessons.md (recurring habits to watch for across stages), and decisions.md (prior venue/track choices) so the plan is personalized and consistent with earlier decisions.
• At end of each stage: append a dated entry via reflect-and-improve/scripts/reflect_log.py — date · orchestrate-paper · stage advanced / blocked, on what signal — and log any venue/track decision to decisions.md.
• Create .paper-memory/ on demand; offer to add it to .gitignore; local only, never uploaded.