dsh-aris-panel 0.1.0

package/skills/research-refine-pipeline/SKILL.md

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+---
+name: research-refine-pipeline
+description: 'Run an end-to-end workflow that chains `research-refine` and `experiment-plan`. Use when the user wants a one-shot pipeline from vague research direction to focused final proposal plus detailed experiment roadmap, or asks to "串起来", build a pipeline, do it end-to-end, or generate both the method and experiment plan together.'
+allowed-tools: Bash(*), Read, Write, Edit, Grep, Glob, WebSearch, WebFetch, mcp__codex__codex, mcp__codex__codex-reply
+---
+
+# Research Refine Pipeline: End-to-End Method and Experiment Planning
+
+Refine and concretize: **$ARGUMENTS**
+
+## Overview
+
+Use this skill when the user does not want to stop at a refined method. The goal is to produce a coherent package that includes:
+
+- a problem-anchored, elegant final proposal
+- the review history explaining why the method is focused
+- a detailed experiment roadmap tied to the paper's claims
+- a compact pipeline summary that says what to run next
+
+This skill composes two existing workflows:
+
+1. `research-refine` for method refinement
+2. `experiment-plan` for claim-driven validation planning
+
+For stage-specific detail, read these sibling skills only when needed:
+
+- `../research-refine/SKILL.md`
+- `../experiment-plan/SKILL.md`
+
+## Core Rule
+
+Do not plan a large experiment suite on top of an unstable method. First stabilize the thesis. Then turn the stable thesis into experiments.
+
+## Default Outputs
+
+- `refine-logs/FINAL_PROPOSAL.md`
+- `refine-logs/REVIEW_SUMMARY.md`
+- `refine-logs/REFINEMENT_REPORT.md`
+- `refine-logs/EXPERIMENT_PLAN.md`
+- `refine-logs/EXPERIMENT_TRACKER.md`
+- `refine-logs/PIPELINE_SUMMARY.md`
+
+## Workflow
+
+### Phase 0: Triage the Starting Point
+
+- Extract the problem, rough approach, constraints, resources, and target venue.
+- Check whether `refine-logs/FINAL_PROPOSAL.md` already exists and still matches the current request.
+- If the proposal is missing, stale, or materially different from the current request, run the full `research-refine` stage.
+- If the proposal is already strong and aligned, reuse it and jump to experiment planning.
+- If in doubt, prefer re-running `research-refine` rather than planning experiments for the wrong method.
+
+### Phase 1: Method Refinement Stage
+
+Run the `research-refine` workflow and keep its V3 philosophy intact:
+
+- preserve the Problem Anchor
+- prefer the smallest adequate mechanism
+- keep one dominant contribution
+- modernize only when it improves the paper
+
+Exit this stage only when these are explicit:
+
+- the final method thesis
+- the dominant contribution
+- the complexity intentionally rejected
+- the key claims and must-run ablations
+- the remaining risks, if any
+
+If the verdict is still `REVISE`, continue into experiment planning only if the remaining weaknesses are clearly documented.
+
+### Phase 2: Planning Gate
+
+Before the experiment stage, write a short gate check:
+
+- What is the final method thesis?
+- What is the dominant contribution?
+- What complexity was intentionally rejected?
+- Which reviewer concerns still matter for validation?
+- Is a frontier primitive central, optional, or absent?
+
+If these answers are not crisp, tighten the final proposal first.
+
+### Phase 3: Experiment Planning Stage
+
+Run the `experiment-plan` workflow grounded in:
+
+- `refine-logs/FINAL_PROPOSAL.md`
+- `refine-logs/REVIEW_SUMMARY.md`
+- `refine-logs/REFINEMENT_REPORT.md`
+
+Ensure the experiment plan covers:
+
+- the main anchor result
+- novelty isolation
+- a simplicity or deletion check
+- a frontier necessity check if applicable
+- run order, budget, and decision gates
+
+### Phase 4: Integration Summary
+
+Write `refine-logs/PIPELINE_SUMMARY.md`:
+
+```markdown
+# Pipeline Summary
+
+**Problem**: [problem]
+**Final Method Thesis**: [one sentence]
+**Final Verdict**: [READY / REVISE / RETHINK]
+**Date**: [today]
+
+## Final Deliverables
+- Proposal: `refine-logs/FINAL_PROPOSAL.md`
+- Review summary: `refine-logs/REVIEW_SUMMARY.md`
+- Experiment plan: `refine-logs/EXPERIMENT_PLAN.md`
+- Experiment tracker: `refine-logs/EXPERIMENT_TRACKER.md`
+
+## Contribution Snapshot
+- Dominant contribution:
+- Optional supporting contribution:
+- Explicitly rejected complexity:
+
+## Must-Prove Claims
+- [Claim 1]
+- [Claim 2]
+
+## First Runs to Launch
+1. [Run]
+2. [Run]
+3. [Run]
+
+## Main Risks
+- [Risk]:
+- [Mitigation]:
+
+## Next Action
+- Proceed to `/run-experiment`
+```
+
+### Phase 5: Present a Brief Summary to the User
+
+```
+Pipeline complete.
+
+Method output:
+- refine-logs/FINAL_PROPOSAL.md
+
+Experiment output:
+- refine-logs/EXPERIMENT_PLAN.md
+- refine-logs/EXPERIMENT_TRACKER.md
+
+Pipeline summary:
+- refine-logs/PIPELINE_SUMMARY.md
+
+Best next step:
+- /run-experiment
+```
+
+## Output Protocols
+
+> Follow these shared protocols for all output files:
+> - **[Output Versioning Protocol](../shared-references/output-versioning.md)** — write timestamped file first, then copy to fixed name
+> - **[Output Manifest Protocol](../shared-references/output-manifest.md)** — log every output to MANIFEST.md
+> - **[Output Language Protocol](../shared-references/output-language.md)** — respect the project's language setting
+
+## Key Rules
+
+- **Large file handling**: If the Write tool fails due to file size, immediately retry using Bash (`cat << 'EOF' > file`) to write in chunks. Do NOT ask the user for permission — just do it silently.
+
+- Do not let the experiment plan override the Problem Anchor.
+- Do not widen the paper story after method refinement unless a missing validation block is truly necessary.
+- Reuse the same claims across `FINAL_PROPOSAL.md`, `EXPERIMENT_PLAN.md`, and `PIPELINE_SUMMARY.md`.
+- Keep the main paper story compact.
+- If the method is intentionally simple, defend that simplicity in the experiment plan rather than adding new components.
+- If the method uses a modern LLM / VLM / Diffusion / RL primitive, make its necessity test explicit.
+- If the method does not need a frontier primitive, say that clearly and avoid forcing one.
+- Prefer the staged skills when the user only needs one stage; use this skill for the integrated flow.
+
+## Composing with Other Skills
+
+```
+/research-refine-pipeline -> one-shot method + experiment planning
+/research-refine   -> method refinement only
+/experiment-plan   -> experiment planning only
+/run-experiment    -> execution
+```

package/skills/research-review/SKILL.md

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+---
+name: research-review
+description: Get a deep critical review of research from an external reviewer backend (Codex or manual). Use when user says "review my research", "help me review", "get external review", or wants critical feedback on research ideas, papers, or experimental results.
+argument-hint: "[topic-or-scope]"
+allowed-tools: Bash(*), Read, Grep, Glob, Write, Edit, mcp__codex__codex, mcp__codex__codex-reply, mcp__manual_review__review, mcp__manual_review__review_reply
+---
+
+# Research Review via External Reviewer Backend (ultra reasoning)
+
+> 🔒 **Do not wrap this skill in `/loop`, `/schedule`, or `CronCreate`.** It is
+> verdict-bearing — it produces a cross-model review verdict, multi-round with
+> reviewer thread continuity. An external timer re-fires the verdict on
+> wall-clock time and breaks the reviewer's round-to-round memory: zero new
+> signal, full token cost. Schedule the *external wait that precedes it* (work
+> ready → then review once), not the verdict. See
+> [`shared-references/external-cadence.md`](../shared-references/external-cadence.md).
+
+Get a multi-round critical review of research work from the selected external reviewer backend with maximum reasoning depth.
+
+## Constants
+
+- REVIEWER_MODEL = `gpt-5.6-sol` — Default model for the Codex backend, reasoning effort `ultra` (deep-audit tier). Must be an OpenAI model (e.g., `gpt-5.6-sol`, `gpt-5.5`, `o3`). Manual backend uses a model the user chooses — it must be a recognized model from a different family (OpenAI, Anthropic, Google, DeepSeek, Moonshot/Kimi, Qwen).
+- **REVIEWER_BACKEND = `codex`** — Default: Codex MCP (ultra). Override with `— reviewer: oracle-pro` for Oracle MCP, or `— reviewer: manual` for Manual Review MCP. If manual-review MCP is unavailable, stop and print the install command; do not fall back to Codex. See `shared-references/reviewer-routing.md`.
+
+## Reviewer Calling Convention
+
+When calling the reviewer, branch on REVIEWER_BACKEND:
+
+**If REVIEWER_BACKEND = `codex`:**
+  Use `mcp__codex__codex` for new review threads.
+  Use `mcp__codex__codex-reply` for follow-up rounds (reuse threadId).
+
+**If REVIEWER_BACKEND = `manual`:**
+  Use `mcp__manual_review__review` for new review threads with:
+    prompt: [exact same prompt that would go to Codex]
+    config: {"model_reasoning_effort": "xhigh", "executor_model": "<actual executor model>", "require_reviewer_model": true}
+  Save the returned `threadId`.
+  Use `mcp__manual_review__review_reply` for follow-up rounds with:
+    threadId: [saved manual-review threadId]
+    prompt: [follow-up prompt]
+    config: {"model_reasoning_effort": "xhigh", "executor_model": "<actual executor model>", "require_reviewer_model": true}
+
+Content fidelity: the manual reviewer should see the same substantive review
+brief Codex would read. If the manual UI supports file upload / attachment,
+reuse the same brief file; otherwise paste the brief contents inline because
+remote web UIs cannot read your local filesystem paths. Review tracing applies
+equally to both backends.
+
+## Context: $ARGUMENTS
+
+## Prerequisites
+
+- **Codex MCP Server** configured in Claude Code:
+  ```bash
+  claude mcp add codex -s user -- codex mcp-server
+  ```
+- This gives Claude Code access to `mcp__codex__codex` and `mcp__codex__codex-reply` tools
+
+## Workflow
+
+### Step 1: Gather Research Context
+Before calling the external reviewer, compile a comprehensive briefing:
+1. Read project narrative documents (e.g., STORY.md, README.md, paper drafts)
+2. Read any memory/notes files for key findings and experiment history
+3. Identify: core claims, methodology, key results, known weaknesses
+
+### Step 2: Initial Review (Round 1)
+Send a detailed prompt with ultra reasoning, using the selected backend. For
+the `codex` backend, keep the MCP payload short: write the full briefing to
+`RESEARCH_REVIEW_REQUEST.md`, then point Codex at that file.
+
+*For codex backend:*
+
+```
+mcp__codex__codex:
+  model: gpt-5.6-sol
+  config: {"model_reasoning_effort": "ultra"}
+  prompt: |
+    Read the review brief at <absolute path to RESEARCH_REVIEW_REQUEST.md>.
+    Executor notes are not evidence beyond the files they cite, so verify the
+    referenced artifacts before judging.
+    Please act as a senior ML reviewer (NeurIPS/ICML level). Start from the
+    assumption that the work is broken somewhere — your job is to find where.
+    Be adversarial. Trust nothing the author tells you — verify everything
+    yourself. Identify:
+    1. Logical gaps or unjustified claims
+    2. Missing experiments that would strengthen the story
+    3. Narrative weaknesses
+    4. Whether the contribution is sufficient for a top venue
+    Please be brutally honest.
+```
+
+The review brief should contain the full research context, the specific
+questions, and the primary artifact / raw-result paths the reviewer should
+inspect.
+
+*For manual backend:* use `mcp__manual_review__review` with the same brief
+contents. If the manual-review UI supports attachments, attach
+`RESEARCH_REVIEW_REQUEST.md`; otherwise paste the brief inline. Save the
+returned `threadId`.
+
+### Step 3: Iterative Dialogue (Rounds 2-N)
+For `codex` backend: use `mcp__codex__codex-reply` with the returned `threadId`.
+For `manual` backend: use `mcp__manual_review__review_reply` with the same `threadId`.
+Use the appropriate tool to continue the conversation. For Codex follow-up
+rounds, write an updated brief such as `RESEARCH_REVIEW_ROUND_2.md` and send
+only the path:
+
+```text
+mcp__codex__codex-reply:
+  threadId: [saved reviewer threadId from Step 2]
+  # replies inherit the thread's model/effort (gpt-5.6-sol ultra)
+  prompt: |
+    Read the updated review brief at <absolute path to
+    RESEARCH_REVIEW_ROUND_2.md>.
+    Focus on unresolved weaknesses and whether the revision actually fixed them.
+```
+
+For manual follow-up rounds, attach that same updated brief if possible;
+otherwise paste it inline.
+
+For each round:
+1. **Respond** to criticisms with evidence/counterarguments
+2. **Ask targeted follow-ups** on the most actionable points
+3. **Request specific deliverables**: experiment designs, paper outlines, claims matrices
+
+Key follow-up patterns:
+- "If we reframe X as Y, does that change your assessment?"
+- "What's the minimum experiment to satisfy concern Z?"
+- "Please design the minimal additional experiment package (highest acceptance lift per GPU week)"
+- "Please write a mock NeurIPS/ICML review with scores"
+- "Give me a results-to-claims matrix for possible experimental outcomes"
+
+### Step 4: Convergence
+Stop iterating when:
+- Both sides agree on the core claims and their evidence requirements
+- A concrete experiment plan is established
+- The narrative structure is settled
+
+### Step 5: Document Everything
+Save the full interaction and conclusions to a review document in the project root:
+- Round-by-round summary of criticisms and responses
+- Final consensus on claims, narrative, and experiments
+- Claims matrix (what claims are allowed under each possible outcome)
+- Prioritized TODO list with estimated compute costs
+- Paper outline if discussed
+
+Update project memory/notes with key review conclusions.
+
+> **Composed mode** — if invoked with `— composed: <canonical-report-path>` (an
+> orchestrator like `/idea-discovery` passes this), do **not** write a standalone review
+> `.md` in the project root. The raw conversation is already persisted to `.aris/traces/…`
+> (see *Review Tracing* below — that audit copy is kept in every mode); fold the review
+> *conclusions* (consensus, claims matrix, prioritized TODOs) into the orchestrator's
+> canonical report and cite the trace path there. **Default (no `— composed:` directive):
+> behave exactly as above — write the standalone review document.** Never infer composed
+> mode from a report file merely existing. Full rules:
+> [`shared-references/output-composition.md`](../shared-references/output-composition.md).
+
+## Key Rules
+
+- ALWAYS pin `model: gpt-5.6-sol` + `config: {"model_reasoning_effort": "ultra"}` for reviews (deep-audit tier; capability fallback per `reviewer-routing.md`, never below `xhigh`)
+- That pin is the **Codex** backend's. For `manual`, use the identity-bearing config from the Reviewer Calling Convention above; `model`, `sandbox` and `cwd` are Codex-only
+- Put comprehensive context in the review brief. Codex can read local files
+  when you pass an absolute path; manual reviewers usually cannot, so attach or
+  paste the same brief there.
+- Be honest about weaknesses — hiding them leads to worse feedback
+- Push back on criticisms you disagree with, but accept valid ones
+- Focus on ACTIONABLE feedback — "what experiment would fix this?"
+- Document the threadId for potential future resumption
+- The review document should be self-contained (readable without the conversation)
+
+## Prompt Templates
+
+### For initial review:
+"I'm going to present a complete ML research project for your critical review. Please act as a senior ML reviewer (NeurIPS/ICML level)..."
+
+### For experiment design:
+"Please design the minimal additional experiment package that gives the highest acceptance lift per GPU week. Our compute: [describe]. Be very specific about configurations."
+
+### For paper structure:
+"Please turn this into a concrete paper outline with section-by-section claims and figure plan."
+
+### For claims matrix:
+"Please give me a results-to-claims matrix: what claim is allowed under each possible outcome of experiments X and Y?"
+
+### For mock review:
+"Please write a mock NeurIPS review with: Summary, Strengths, Weaknesses, Questions for Authors, Score, Confidence, and What Would Move Toward Accept."
+
+## Review Tracing
+
+After each reviewer call (`mcp__codex__codex`, `mcp__codex__codex-reply`, `mcp__manual_review__review`, or `mcp__manual_review__review_reply`), save the trace following `shared-references/review-tracing.md` (Policy C — forensic; never silently skip). Use `save_trace.sh` (resolved per the chain in `shared-references/integration-contract.md` §2) or write files directly to `.aris/traces/<skill>/<date>_run<NN>/`. Respect the `--- trace:` parameter (default: `full`).
+  A verdict-bearing manual response MUST begin with
+  `Reviewer-Model: <exact-model-id>` — pass the model THIS session is actually
+  running as in `executor_model`. Missing, unknown, or same-family identity
+  cannot acquit; emit `REVIEW_UNAVAILABLE` rather than guessing. If the executor
+  model cannot be named, manual review's cross-family claim is unprovable — say
+  so in the report instead of asserting it.