Deep Research

Hypothesis-driven research swarm. Spawns specialist agents to investigate a task, grades every finding by evidence quality, then adversarially challenges the emerging conclusion before delivering a structured verdict.

When This Skill Activates

Trigger on explicit research requests:

User says: "research", "investigate", "discover", "how should I approach..."
User asks: "what's the best way to...", "explore options for...", "deep research"
User wants prior art, feasibility analysis, or approach comparison

Do NOT activate automatically on every task. This is an on-demand tool, not a gate.

Phase 1: Hypothesis Formation

Before spawning agents, frame the research:

Parse the task: Extract the core question or goal. If ambiguous, ask the user to clarify before proceeding. Identify technology keywords (languages, frameworks, libraries mentioned or implied by the codebase).
Identify repo context: Run git rev-parse --show-toplevel to get {repo_root}. If this fails (not a git repo), set {repo_root} to the current working directory. Check for package.json, pyproject.toml, Cargo.toml, go.mod, etc. to identify the language/framework stack. Pass this as {tech_stack}. If no manifests are found, set {tech_stack} to the primary file extensions present or ask the user.
speak-memory: If .speak-memory/index.md exists and an active story matches the current work, read it for context. If .speak-memory/ does not exist, skip.
Form hypotheses: State 1-3 hypotheses to investigate. For each:
- Question: The specific question being answered
- Prior belief: What you expect the answer to be (best guess before research)
- Disconfirming evidence: What evidence would change the answer
If the task is open-ended ("how should I build X?") and you have no prior belief, that's fine — set prior belief to "unknown" and frame the hypothesis as: "There is an established approach for X in this codebase/ecosystem." Disconfirming evidence: "No established patterns exist; this is novel."
Set scope budget: Declare upfront: "Budget: 5 research agents + 1 adversarial challenge = 6 agent calls, investigating N hypotheses." (substitute the actual hypothesis count for N). When budget is exhausted, synthesize what you have rather than expanding.

Present hypotheses to the user before proceeding:

Hypotheses:
1. [Question] — Prior belief: [X]. Would change if: [Y].
2. ...

Budget: 6 agents, [hypothesis count] questions. Proceed?

If the user declines or asks to revise, update the hypotheses and re-present. Do not spawn agents until the user confirms.

Phase 2: Evidence Gathering

Spawn all 5 agents in a single message (parallel Agent tool calls). Each agent returns a JSON findings array — see references/agent-roles.md for full prompts.

Agent	Subagent Type	Model	Focus
codebase	Explore	opus	Existing patterns, utilities, similar implementations, conventions
web-research	general-purpose	opus	Solutions, libraries, best practices, documentation
tools-mcp	general-purpose	opus	Available MCP servers, tools, and resources
skills	general-purpose	opus	Installed skills and marketplace matches
dependencies	general-purpose	opus	Installed packages, version constraints, compatibility

Agent tool grants:

codebase: Read, Glob, Grep (read-only codebase exploration)
web-research: WebSearch, WebFetch (external research)
tools-mcp: ListMcpResourcesTool, ReadMcpResourceTool (tool discovery)
skills: Read, Glob, Grep, Bash (read skills + npx skills find)
dependencies: Read, Glob, Grep, Bash (read manifests + npm ls/pip list/cargo tree)

Pass each agent the hypotheses so they can focus their search, but instruct them to also report unexpected relevant findings outside the hypothesis scope.

Required output format (every finding must include evidence_tier):

[
  {
    "evidence_tier": "primary|secondary|speculative",
    "relevance": "high|medium|low",
    "source": "where this was found (file path, URL, tool name)",
    "finding": "what was discovered",
    "supports_hypothesis": "which hypothesis this relates to, or 'unexpected'",
    "recommendation": "how this finding applies to the task",
    "references": ["file paths or URLs for further reading"]
  }
]

Evidence tiers:

primary: Direct from authoritative source — code you read, API response, official documentation, test output
secondary: Reputable third-party — blog post with evidence, SO answer with code examples, well-maintained library README
speculative: Inference, analogy, or "I think" — no direct source confirms this

Return empty array [] if no relevant findings in that domain.

Instruct each agent: "Return your top 10 findings maximum, prioritized by relevance. Tag every finding with an evidence_tier. Never report speculative findings as primary."

Error handling: If an agent returns non-JSON output, strip code fences and attempt JSON extraction. If extraction fails or the agent times out, treat as empty array [] and log a warning. Continue with results from agents that succeeded.

Phase 3: Synthesis

Merge all 5 finding arrays. Apply the synthesis rules from references/synthesis.md:

Merge: Collect all 5 JSON arrays into a single flat array. Tag each finding with its source agent name. Note which agents failed or returned empty.
Deduplicate: Merge identical findings; note corroborating sources.
Resolve conflicts: Flag when agents disagree; note the resolution.
Grade evidence: Flag any conclusion that rests entirely on speculative evidence. A conclusion needs at least one primary or secondary source to be credible.
Rank: Sort by evidence_tier (primary first), then relevance, then corroboration. Cap the merged array at 30 findings — drop low-relevance speculative findings first to keep context manageable.
Form preliminary conclusion: Based on the ranked findings, form a preliminary answer to each hypothesis. State whether the prior belief was confirmed or changed.
Generate approaches: Propose 2-3 approaches with trade-offs. Each approach must reference the evidence that supports it with tier tags.

Phase 4: Adversarial Challenge

Before delivering findings, actively try to disprove the emerging conclusion.

Spawn one devil's advocate agent (subagent_type: "general-purpose", model: "opus"). Give it:

The preliminary conclusion from Phase 3
The recommended approach
The hypotheses and their current status (confirmed/changed)

The devil's advocate agent's job:

Search for disconfirming evidence using WebSearch, WebFetch, Read, Glob, Grep
Find reasons the recommended approach would fail
Identify assumptions that haven't been tested
Look for alternatives the research may have missed

See references/agent-roles.md for the full devil's advocate prompt.

Handle the devil's advocate result:

conclusion_holds: The conclusion survives — it's stronger. Note any speculative counterarguments as dissent but don't change the recommendation.
conclusion_weakened: The devil's advocate found credible disconfirming evidence (primary or secondary tier). Revise the conclusion, note the revision, and re-generate approaches (re-run synthesis Step 7) to reflect the updated position.
conclusion_overturned: The recommended approach is fundamentally flawed. Discard it, revise all affected hypothesis conclusions, and re-generate approaches from scratch based on the combined original + adversarial evidence.

Error handling: If the devil's advocate agent fails (non-JSON output, timeout, or invalid structure), log a warning: "Devil's advocate failed — conclusion not adversarially tested. Reduce confidence by one level." Continue to Phase 5 with the untested conclusion.

Phase 5: Verdict

Output a structured verdict (use assets/report-template.md for formatting):

VERDICT: [one sentence answer]
CONFIDENCE: high|medium|low — [justification]
EVIDENCE:
  1. [primary] source — finding
  2. [secondary] source — finding
  3. ...
DISSENT: [strongest counterargument from devil's advocate]
ACTION: [what to do next — implement X, investigate Y further, do nothing]

After the verdict, output the structured artifact for downstream skills:

{
  "task": "original task description",
  "tech_stack": ["identified technologies"],
  "hypotheses": [
    {
      "question": "...",
      "prior_belief": "...",
      "conclusion": "confirmed|changed|inconclusive",
      "conclusion_detail": "what we found"
    }
  ],
  "metadata": {
    "agents_completed": ["codebase", "web-research", "tools-mcp", "skills", "dependencies", "devils-advocate"],
    "agents_failed": [],
    "total_findings": 0,
    "speculative_only_conclusions": 0,
    "timestamp": "ISO-8601"
  },
  "findings": [... merged findings array (high/medium only, with evidence_tier) ...],
  "conflicts": [
    {
      "description": "what conflicts",
      "agents": ["which agents disagree"],
      "resolution": "how resolved, or null if user must decide"
    }
  ],
  "verdict": {
    "summary": "one sentence",
    "confidence": "high|medium|low",
    "confidence_justification": "why this confidence level",
    "dissent": "strongest counterargument"
  },
  "approaches": [
    {
      "name": "Approach A",
      "summary": "one-line description",
      "pros": ["..."],
      "cons": ["..."],
      "recommended": true,
      "evidence": ["[primary] source — finding", "..."],
      "relevant_files": ["paths from codebase agent"],
      "relevant_tools": ["MCP tools/skills discovered"],
      "dependencies_needed": ["new packages, if any"],
      "estimated_complexity": "low|medium|high"
    }
  ]
}

No-findings edge case: If all agents return empty arrays, output the structured artifact with findings: [], approaches: [], and verdict.confidence: "low". Set verdict.summary to: "Research found no directly relevant prior art. Recommend exploratory implementation or breaking the task into smaller sub-problems."

speak-memory: If an active story was loaded in Phase 1, use Write/Edit to update the story file — append to Recent Activity and update Current Context.

Key Constraints

All research agents: Opus (model: "opus") for maximum research quality.
Agent execution caps: Research agents: max_turns: 30. Devil's advocate: max_turns: 20.
Max 2 levels of nesting: orchestrator → specialist. Specialists never spawn agents.
Scope budget: 5 research agents + 1 devil's advocate = 6 total. Do not expand.
Findings cap: Max 30 findings enter synthesis (after merge + dedup). Drop low-relevance speculative findings first.
All sub-agents are read-only — no code modifications, no git changes. The orchestrator may write to .speak-memory/ only.
Bash (sub-agents only) limited to dependency queries (npm ls, pip list, cargo tree) and skill search (npx skills find). No other Bash commands.
Conclusions resting entirely on speculative evidence must be flagged as low confidence.
The structured artifact stays in conversation context — no file writing.

Closing Checklist

Do not declare the research done until all boxes are checked:

Hypotheses stated with prior beliefs and disconfirming criteria
All 5 research agents completed (returned valid JSON) or failed (logged as warning)
Every finding tagged with evidence_tier (primary/secondary/speculative)
Preliminary conclusion formed and approaches generated
Devil's advocate challenged the conclusion
Structured verdict delivered (verdict, confidence, evidence, dissent, action)
Structured artifact output for downstream consumption
speak-memory story updated (if applicable)

Reference Files

Load only when needed:

references/agent-roles.md — Full prompt templates for each research agent + devil's advocate
references/synthesis.md — Evidence grading, dedup, conflict resolution, approach generation
assets/report-template.md — Verdict and report format

deep-research