ars-bootstrap

Academic Research Skills — Copilot CLI

A suite of Copilot CLI skills for rigorous academic research, paper writing, peer review, and pipeline orchestration.

Extension Setup Check (run once, idempotent)

Step 0 — Silent exit gate (prevents repeated prompts):

Check: does ~/.copilot/extensions/ars/.bootstrapped exist?

• If YES → extension was previously registered. Exit silently — do NOT display any of the setup instructions below. The rest of this bootstrap skill (skills overview, routing rules, trigger keywords) should still be loaded into agent context, but no user-facing setup message is shown.
• If NO → proceed to Step 1 below for first-time setup.

Step 1 — First-time setup (only when .bootstrapped is missing):

On first invocation, verify the ARS extension is registered:

Check: does ~/.copilot/extensions/ars/extension.mjs exist? (use test -L ~/.copilot/extensions/ars/extension.mjs or equivalent)

If the file does NOT exist:

1. Resolve the plugin install directory from the location of this SKILL.md: PLUGIN_DIR=$(dirname $(dirname $(readlink -f skills/ars-bootstrap/SKILL.md)))
2. Run the setup script: bash "${PLUGIN_DIR}/scripts/setup-copilot-extension.sh"
3. The setup script creates the symlink AND the .bootstrapped marker.
4. Call extensions_reload({}) to reload extensions. The 13 slash commands are activated immediately within the same session.

If the file EXISTS but .bootstrapped is missing (edge case: manual symlink):

1. Create the marker: touch ~/.copilot/extensions/ars/.bootstrapped
2. Then exit silently.

After setup is complete and .bootstrapped exists, the bootstrap skill runs silently on every subsequent session — routing rules are injected into agent context without any user-facing prompt.

Skills Overview

Skill	Purpose	Key Modes
deep-research v2.9.4	13-agent research team	full, quick, socratic, review, lit-review, fact-check, systematic-review
academic-paper v3.1.2	12-agent paper writing	full, plan, outline-only, revision, revision-coach, abstract-only, lit-review, format-convert, citation-check, disclosure
academic-paper-reviewer v1.9.1	Multi-perspective paper review (5 reviewers + optional cross-model DA critique)	full, re-review, quick, methodology-focus, guided, calibration
academic-pipeline v3.11.1	Full pipeline orchestrator	(coordinates all above)

Trigger Auto-Detection

English keywords:

• Research: research, literature review, systematic review, fact-check, research proposition
• Writing: write my paper, academic paper, revise my paper, format conversion, abstract
• Reviewing: peer review, manuscript review, referee report, critique paper
• Pipeline: full pipeline, end-to-end, research to publication, complete workflow

中文關鍵詞:

• 研究: 研究, 深度研究, 文獻回顧, 事實查核, 研究方向
• 寫作: 論文寫作, 學術論文, 期刊論文, 修改論文, 寫摘要
• 審核: 審查意見, 審稿回覆, 模擬審查
• 流程: 完整流程, 從頭到尾, 研究到論文

Model Routing (Optional)

ARS supports tiered model dispatch via environment variables for BYOK users:

# Architect tier (complex reasoning: full pipeline, revision-coach, reviewer)
export ARS_MODEL_ARCHITECT="claude-opus-4-5"

# Execution tier (focused tasks: plan, outline, revision, abstract, etc.)
export ARS_MODEL_EXECUTION="claude-sonnet-4-5"

How it works:

• CommandDefinition handlers check ARS_MODEL_ARCHITECT / ARS_MODEL_EXECUTION env vars
• If set, the dispatch prompt includes task({model: "<value>"}) for subagent dispatches
• If not set, all dispatches use the session default model (no routing)
• Model routing works within a single provider's model family (e.g., both opus and sonnet on Anthropic)
• Set COPILOT_PROVIDER_BASE_URL, COPILOT_PROVIDER_TYPE, COPILOT_PROVIDER_API_KEY, and COPILOT_MODEL for BYOK

Pipeline State Machine

deep-research (socratic/full)
  → academic-paper (plan/full)
    → integrity check (Stage 2.5)
      → academic-paper-reviewer (full/guided)
        → academic-paper (revision)
          → academic-paper-reviewer (re-review, max 2 loops)
            → final integrity check (Stage 4.5)
              → academic-paper (format-convert → final output)
                → Process Summary + AI Self-Reflection Report

Routing Discipline (v3.9.2)

Routing precedence: This section runs BEFORE Routing Rules 1-5. Once this section settles on a destination, Rules 1-5 apply within that destination's skill family.

Step 0 — Escape hatch check (before any classification): If the user's first message begins with [direct-mode] (case-insensitive byte-0 token, optionally preceded by whitespace/newlines that are stripped on parse), record this fact, strip the prefix and surrounding whitespace from the message, and skip directly to Step 1 explicit-intent handling on the stripped content. The literal [direct-mode] is NOT passed through to the dispatched agent. If the stripped message itself has no clear skill named, Step 1 falls through to Step 3 clarification (the escape hatch bypasses cross-phase clarification (Step 2), not all routing).

Otherwise, classify the user's input:

1. Explicit clear intent — user invokes a specific skill via /ars-* slash command, /academic-research-skills:* auto-command, or uses an unambiguous trigger keyword that maps to a single skill (e.g., "lit-review this", "review my paper", "draft an abstract"): → Route directly; no clarification, no orchestrator detour.

2. Cross-phase materials detected — user provides artifacts spanning ≥ 2 pipeline phases without naming a specific skill (e.g., pre-written abstract + pre-collected literature; full draft + reviewer comments + bibliography): → Clarify. Do NOT auto-route to a single-phase agent. List candidate workflows as a-d options in markdown body. See shared/references/intent_clarification_protocol.md for the message template.

3. Ambiguous intent, no materials — user provides no artifacts and no clear request: → Clarify per shared/references/intent_clarification_protocol.md.

Anti-pattern: Receiving ambiguous cross-phase materials and silently auto-routing to a single-phase agent based on which phase the materials "look closest to." This bypasses orchestrator-level reconciliation.

Forward note (v3.10): Active conductor (#134) will reframe this gate as structured intake with task envelope dispatch. v3.9.2 ships clarification-only as interim hot-fix.

Routing Rules

1. academic-pipeline vs individual skills: academic-pipeline = full pipeline orchestrator (research → write → integrity → review → revise → final integrity → finalize). If the user only needs a single function (just research, just write, just review), trigger the corresponding skill directly without the pipeline.

2. deep-research vs academic-paper: Complementary. deep-research = upstream research engine (investigation + fact-checking), academic-paper = downstream publication engine (paper writing + bilingual abstracts). Recommended flow: deep-research → academic-paper.

3. deep-research socratic vs full: socratic = guided Socratic dialogue to help users clarify their research question. full = direct production of research report. When the user's research question is unclear, suggest socratic mode.

4. academic-paper plan vs full: plan = chapter-by-chapter guided planning via Socratic dialogue. full = direct paper production. When the user wants to think through their paper structure, suggest plan mode.

5. academic-paper-reviewer guided vs full: guided = Socratic review that engages the author in dialogue about issues. full = standard multi-perspective review report. When the user wants to learn from the review, suggest guided mode.

Key Rules

• All claims must have citations
• Evidence hierarchy respected (meta-analyses > RCTs > cohort > case reports > expert opinion)
• Contradictions disclosed with evidence quality comparison
• AI disclosure in all reports
• Default output language matches user input (Traditional Chinese or English)
• Agent dispatch: Use task({agent_type: "general-purpose", prompt: <agent template content>}) to dispatch sub-agents. Load agent templates from deep-research/agents/, academic-paper/agents/, academic-paper-reviewer/agents/, and academic-pipeline/agents/ directories.

Handoff Protocol

deep-research → academic-paper

Materials: RQ Brief, Methodology Blueprint, Annotated Bibliography, Synthesis Report, INSIGHT Collection

academic-paper → academic-paper-reviewer

Materials: Complete paper text. field_analyst_agent auto-detects domain and configures reviewers.

academic-paper-reviewer → academic-paper (revision)

Materials: Editorial Decision Letter, Revision Roadmap, Per-reviewer detailed comments

Version Info

• Suite version: 3.11.1-copilot
• Last Updated: 2026-05-28
• Author: Zhenyu Zhang
• License: CC-BY-NC 4.0