Deep Research

Deep Research

A three-phase evidence-gathering workflow for problems where getting the design wrong is expensive: safety-critical code, performance-critical paths, distributed systems protocols, unsafe Rust, concurrency primitives, and novel algorithms.

Research agents independently survey the landscape (papers, production systems, post-mortems, specifications), a synthesizer cross-references and ranks the evidence, and an integrator maps findings to a concrete implementation plan grounded in the codebase.

When to Use

• Safety-critical: unsafe blocks, memory management, lock-free data structures
• Performance-critical: hot-path algorithms, cache-aware layouts, SIMD strategies
• Distributed systems: consensus, replication, failure detection, ordering
• Novel or unfamiliar territory: algorithms you haven't implemented before
• High-stakes design decisions: choices that are expensive to reverse
• Concurrency: lock strategies, atomic ordering, async runtime interactions

When NOT to Use

• Straightforward CRUD features or wiring code
• Problems with a single obvious solution
• Tasks where you already have deep domain expertise and just need to code
• Use design-tournament instead when the problem is well-understood but multiple valid approaches exist

Invocation

deep-research <problem statement>

The <problem statement> should describe what you're trying to build or decide, and why existing knowledge is insufficient. If no argument is given, ask the user for the problem statement before proceeding.

Phase 1 — Research (3-5 Parallel Agents)

Launch 5 research agents in parallel using the Codex agent tools (spawn_agent, send_input, wait) with agent_type=default. Each agent has a distinct research lens but receives the same problem statement. All agents explore the codebase for context AND search the web for external evidence.

All 5 agents MUST be launched in a single message (one message, five spawn_agent calls) so they run concurrently.

Research Agent Specialties

Each agent receives the common preamble below, with {PROBLEM} replaced by the user's problem statement, {AGENT_ID} set to its label, and {SPECIALTY} / {FOCUS} set per-agent.

Common Preamble (included in every agent's prompt)

You are Research Agent {AGENT_ID} — a {SPECIALTY} specialist.

## Problem Under Investigation
{PROBLEM}

## Your Research Mission

You are one of 5 independent research agents. Your job is to gather HARD
EVIDENCE — not opinions — about how this problem has been solved before.
Every claim must have a source. Unsourced claims are worthless.

### Research Process

1. **Understand the codebase context**: Use `rg --files`, `rg`, and targeted file reads to understand
   the relevant parts of the codebase. What exists today? What constraints does
   the current architecture impose?

2. **Search for external evidence**: Use `web.search_query` and `web.open` to find:
   - Academic papers and technical reports
   - Documentation from production systems that solve similar problems
   - RFCs, specifications, and formal descriptions
   - Post-mortems and failure analyses
   - Conference talks, technical blog posts from credible sources
   - Existing open-source implementations

3. **Evaluate and document**: For each piece of evidence, record:
   - Source (URL, paper title, system name)
   - Key finding or technique
   - Relevance to our specific problem
   - Evidence strength (see scale below)

### Evidence Strength Scale

| Level | Label | Description | Example |
|-------|-------|-------------|---------|
| 5 | **Proven at scale** | Battle-tested in production systems handling similar workloads | FoundationDB's simulation testing, TigerBeetle's storage engine |
| 4 | **Peer-reviewed** | Published in reputable venue with formal analysis | OSDI/SOSP paper with proofs |
| 3 | **Implemented & tested** | Open-source implementation with benchmarks/tests | Well-maintained crate with >1k stars, comprehensive test suite |
| 2 | **Documented practice** | Technical blog from credible engineering org | Blog post from Cloudflare, Datadog, AWS engineering |
| 1 | **Anecdotal** | Forum discussion, personal blog, Stack Overflow answer | Useful for leads but needs corroboration |

### Focus Area
{FOCUS}

### Rules

- EVERY finding must have a concrete source. No source = don't include it.
- Prefer primary sources over secondary summaries.
- If you find contradictory evidence, report BOTH sides with sources.
- Distinguish between "X is theoretically optimal" and "X works in production."
- Note when evidence is from a different domain and may not transfer directly.
- Search for COUNTER-evidence too — what are the failure modes of popular approaches?
- If a search returns no useful results, say so. Do not fabricate references.

### Output Format

Return a markdown document starting with:
`# Research Report — Agent {AGENT_ID}: {SPECIALTY}`

Then these sections:

#### 1. Codebase Context
What you found in the current codebase that's relevant. File paths and line
numbers for key structures.

#### 2. Findings
For each piece of evidence (aim for 5-15 findings):

**Finding {N}: {title}**
- **Source**: {URL or citation}
- **Evidence strength**: {1-5} — {label}
- **Summary**: {2-4 sentences}
- **Key technique/insight**: {the actionable takeaway}
- **Applicability to our problem**: {high/medium/low} — {why}
- **Caveats**: {limitations, different assumptions, scaling concerns}

#### 3. Patterns & Consensus
What approaches appear repeatedly across sources? Where do experts agree?

#### 4. Disagreements & Open Questions
Where do sources contradict each other? What remains unresolved?

#### 5. Recommended Reading
Top 3-5 sources the team should read, ranked by relevance.

Agent 1 — Foundational Theory

{SPECIALTY}: Foundational Theory & Algorithms
{FOCUS}:
Search for the THEORETICAL foundations of this problem:
- Seminal papers and algorithms (Lamport, Dijkstra, Knuth, etc.)
- Formal correctness proofs or verification approaches
- Complexity bounds — what's provably optimal?
- Mathematical models and invariants
- Type-theoretic or formal methods approaches

Start with `web.search_query` queries like:
- "{problem keywords} algorithm formal proof"
- "{problem keywords} paper OSDI SOSP VLDB SIGMOD"
- "{problem keywords} correctness verification"
- "{problem keywords} complexity bounds"

Look at:
- arxiv.org, dl.acm.org, usenix.org proceedings
- PhD theses and technical reports
- Textbook chapters (CLRS, TAOCP, etc.)

Agent 2 — Production Systems

{SPECIALTY}: Production Systems & Battle-Tested Implementations
{FOCUS}:
Search for how REAL SYSTEMS in production solve this problem:
- Database engines (FoundationDB, TigerBeetle, CockroachDB, SQLite, DuckDB)
- Storage systems (RocksDB, LevelDB, WiscKey)
- Distributed systems (etcd, Raft implementations, Paxos variants)
- High-performance systems (DPDK, SPDK, io_uring users)
- Language runtimes (Go GC, Rust allocators, JVM internals)
- Operating systems (Linux kernel, FreeBSD, Fuchsia)

Start with `web.search_query` queries like:
- "{problem keywords} implementation production"
- "{system name} {problem keywords} design"
- "{problem keywords} source code github"
- "how does {system} handle {problem}"

For each system found:
- What approach do they use?
- What scale does it operate at?
- What trade-offs did they make and why?
- Link to source code or design docs when available.

Agent 3 — Failure Modes & Pitfalls

{SPECIALTY}: Failure Modes, Post-Mortems & Anti-Patterns
{FOCUS}:
Search for how this problem GOES WRONG:
- Post-mortems from outages caused by similar systems
- CVEs and security advisories in related implementations
- Known anti-patterns and common mistakes
- Performance cliffs and degenerate cases
- Subtle bugs found in production (Jepsen reports, fuzzing results)
- Memory safety issues in similar C/C++/Rust implementations

Start with `web.search_query` queries like:
- "{problem keywords} bug post-mortem"
- "{problem keywords} vulnerability CVE"
- "{problem keywords} performance regression"
- "{problem keywords} Jepsen analysis"
- "{problem keywords} common mistakes pitfalls"
- "{problem keywords} undefined behavior unsafe"

For each failure found:
- What went wrong?
- Root cause analysis
- How was it detected?
- How was it fixed or mitigated?
- What invariant was violated?

Agent 4 — Rust Ecosystem & Implementation Patterns

{SPECIALTY}: Rust Ecosystem & Implementation Patterns
{FOCUS}:
Search for how this problem is solved IN RUST specifically:
- Existing crates that address this problem (crates.io, lib.rs)
- Rust-specific patterns (ownership for safety, typestate, const generics)
- Unsafe code patterns and safety proofs in similar Rust projects
- Benchmarks comparing Rust implementations
- Rust RFCs and compiler internals if relevant

Start with `web.search_query` queries like:
- "{problem keywords} rust crate"
- "{problem keywords} rust implementation"
- "{problem keywords} rust unsafe safe abstraction"
- "{problem keywords} rust performance benchmark"
- "crates.io {problem keywords}"

For each crate or pattern found:
- API design — how is it exposed to users?
- Safety story — how is unsafe (if any) encapsulated?
- Performance characteristics — any benchmarks?
- Maintenance status — actively maintained? Production users?
- Code quality — tests, docs, CI, fuzzing?

Also check the Rust standard library and popular foundational crates
(crossbeam, tokio, rayon, parking_lot, etc.) for relevant patterns.

Agent 5 — Industry Practice & Architecture

{SPECIALTY}: Industry Practice & System Architecture
{FOCUS}:
Search for how ENGINEERING ORGANIZATIONS approach this problem:
- Technical blog posts from major engineering orgs (Google, Meta, AWS,
  Cloudflare, Datadog, Discord, Figma, Fly.io)
- Conference talks (Strange Loop, RustConf, P99 CONF, QCon)
- Architecture Decision Records (ADRs) in open-source projects
- RFCs and design documents from relevant projects
- Books and practitioner guides

Start with `web.search_query` queries like:
- "{problem keywords} engineering blog"
- "{problem keywords} architecture design document"
- "{problem keywords} conference talk"
- "{problem keywords} RFC design"
- "{problem keywords} lessons learned"
- "{problem keywords} at scale"

For each practice found:
- What organization or project uses this approach?
- At what scale?
- What alternatives did they evaluate?
- What would they do differently in hindsight?
- Is this approach specific to their constraints or generalizable?

Collecting Results

After all 5 agents complete, gather their outputs. If any agent fails or times out, proceed with the agents that succeeded (minimum 3 required for Phase 2).

Phase 2 — Synthesize (Single Agent)

Launch 1 synthesis agent using the Codex agent tools (spawn_agent, send_input, wait) with agent_type=default.

Synthesizer Prompt

You are the Research Synthesizer. Five independent research agents have
investigated the same problem from different angles. Your job is to
cross-reference their findings into a single, evidence-ranked knowledge base.

## Original Problem
{PROBLEM}

## Research Reports
{ALL_FIVE_REPORTS}

## Your Task

### 1. Evidence Inventory

Create a master list of ALL unique findings across all 5 agents. For
findings reported by multiple agents, merge them and note corroboration.

For each finding:
- **ID**: F{N}
- **Title**: {descriptive title}
- **Sources**: {all sources citing this finding, with URLs}
- **Corroboration**: {how many agents independently found this}
- **Evidence strength**: {1-5, use the highest-quality source}
- **Applicability**: {high/medium/low for our specific problem}

### 2. Consensus Matrix

Identify the key design decisions for this problem, then for each decision
show where the evidence points:

| Decision | Option A | Option B | Evidence For A | Evidence For B | Verdict |
|----------|----------|----------|----------------|----------------|---------|

The verdict should be: STRONG CONSENSUS, LEAN (direction), CONTESTED, or
INSUFFICIENT EVIDENCE.

### 3. Evidence-Ranked Techniques

Rank all discovered techniques/approaches by weighted evidence score:

Score = (evidence_strength × applicability × corroboration_count)

| Rank | Technique | Score | Evidence | Applicability | Corroboration | Key Source |
|------|-----------|-------|----------|---------------|---------------|------------|

### 4. Risk Register

From the failure modes research, compile a risk register:

| Risk ID | Risk | Likelihood | Impact | Mitigation | Source |
|---------|------|------------|--------|------------|--------|

### 5. Contradictions & Gaps

- Where do sources disagree? What's the strongest evidence on each side?
- What aspects of the problem have NO evidence? Where are we flying blind?
- What evidence exists but doesn't transfer to our specific context?

### 6. Key Insights

The 5-10 most important things learned from this research that should
directly influence the design. Each must cite at least one source.

### Rules

- Do NOT add your own findings — you are synthesizing, not researching.
- If an agent's finding has no source, downgrade it to evidence strength 0
  and flag it as UNVERIFIED.
- Preserve ALL source URLs from the original reports.
- If agents contradict each other, present both sides — do not pick a winner
  unless the evidence clearly favors one side.
- Be explicit about what we DON'T know, not just what we do.

### Output Format

Return a markdown document starting with:
`# Research Synthesis`

Include all sections above, plus a final section:

#### Executive Summary
3-5 bullet points capturing the most critical findings for someone who
won't read the full report.

Phase 3 — Integrate (Single Agent)

Launch 1 integration agent using the Codex agent tools (spawn_agent, send_input, wait) with agent_type=default.

This agent maps the synthesized research to a concrete implementation plan grounded in the actual codebase.

Integrator Prompt

You are the Research-to-Plan Integrator. You have a comprehensive research
synthesis and access to the codebase. Your job is to produce a concrete,
evidence-backed implementation plan.

## Original Problem
{PROBLEM}

## Research Synthesis
{SYNTHESIS_REPORT}

## Your Task

### Step 1: Codebase Mapping

Thoroughly explore the codebase to understand:
- Current architecture and module structure (use `rg --files`, `rg`, and targeted file reads)
- Existing patterns and conventions
- What infrastructure already exists that can be leveraged
- What constraints the current architecture imposes
- Dependencies and their versions

Map each research finding to specific locations in the codebase:
- Which files/modules would be affected?
- What existing abstractions can be reused?
- Where do new abstractions need to be introduced?

### Step 2: Implementation Plan

Produce a step-by-step implementation plan where EVERY design decision
cites evidence from the synthesis:

#### Plan Format

For each step:

**Step {N}: {title}**
- **What**: {concrete description — types, signatures, module placement}
- **Why**: {justification citing specific findings by ID: F1, F7, etc.}
- **Evidence**: {the specific technique/paper/system this is based on}
- **Files**: {exact file paths to create or modify}
- **Risks**: {from the risk register, with mitigation}
- **Acceptance criteria**: {how to verify this step is correct}

### Step 3: Evidence Trail

Create a traceability matrix:

| Plan Step | Research Finding(s) | Evidence Strength | Confidence |
|-----------|--------------------|--------------------|------------|

Confidence levels:
- HIGH: Multiple strong sources agree, directly applicable
- MEDIUM: Evidence exists but from different context, or sources disagree
- LOW: Limited evidence, based on extrapolation
- NOVEL: No direct evidence found — this is our own design (flag for extra review)

Any step with LOW or NOVEL confidence gets a mandatory note explaining
what additional validation is needed (benchmarks, property tests, fuzzing,
formal verification, etc.).

### Step 4: Alternative Approaches

For any CONTESTED decisions from the synthesis, describe:
- The alternative approach
- What evidence supports it
- Under what conditions we'd switch to it
- How to structure the code so switching is feasible

### Step 5: Validation Strategy

How to verify the implementation is correct:
- What properties should be tested (unit, property-based, fuzz)?
- What benchmarks should be run?
- What failure modes from the risk register need explicit test cases?
- Are there formal verification opportunities (Kani, MIRI)?

### Rules

- Every design decision MUST cite evidence. If there's no evidence for a
  choice, flag it explicitly as NOVEL/UNJUSTIFIED.
- Be concrete: file paths, type signatures, function names. Not hand-waving.
- Respect existing codebase conventions — don't propose patterns alien to
  the project.
- The plan should be implementable by a developer who hasn't read the full
  research — include enough context in each step.
- Include estimated complexity per step (S/M/L) but NOT time estimates.

### Output Format

Return a markdown document starting with:
`# Implementation Plan`

Include all sections above, plus:

#### References
A numbered bibliography of all sources cited in the plan, with URLs.
Each citation in the plan body should reference this list: [1], [2], etc.

Final Output Format

After the integrator completes, present the combined output to the user:

## Deep Research Results

### Problem
{one-line restatement}

### Executive Summary
{from the synthesizer's executive summary}

### Evidence Highlights
| # | Finding | Evidence Strength | Sources | Applicability |
|---|---------|-------------------|---------|---------------|
{top 10 findings from the synthesis, ranked by score}

### Implementation Plan
{the integrator's full plan}

### Consensus & Contested Decisions
{consensus matrix from the synthesis}

### Risk Register
{risk register from the synthesis}

### Full Research (collapsed)
<details><summary>Research Agent 1: Foundational Theory</summary>
{full report}
</details>
<details><summary>Research Agent 2: Production Systems</summary>
{full report}
</details>
<details><summary>Research Agent 3: Failure Modes & Pitfalls</summary>
{full report}
</details>
<details><summary>Research Agent 4: Rust Ecosystem</summary>
{full report}
</details>
<details><summary>Research Agent 5: Industry Practice</summary>
{full report}
</details>
<details><summary>Full Research Synthesis</summary>
{synthesis report}
</details>

### References
{consolidated bibliography from integrator}

Configuration

Default: 5 researchers + 1 synthesizer + 1 integrator (7 total agents).

The user can reduce the research agents:

deep-research 3 agents: <problem>

Enforce these limits:

• Phase 1: minimum 3 research agents, maximum 5
• If 3 agents: use agents 1 (Theory), 2 (Production Systems), 3 (Failure Modes)
• If 4 agents: add agent 4 (Rust Ecosystem)
• If 5 agents: all five (default)
• Phase 2: always exactly 1 synthesizer
• Phase 3: always exactly 1 integrator

Tips

• Include relevant file paths or module names in the problem statement so research agents can examine the codebase for context.
• For distributed systems problems, the Failure Modes agent (Agent 3) is critical — never reduce below 3 agents.
• The output from this skill feeds naturally into design-tournament if you want to explore multiple implementation approaches after research.
• For unsafe Rust, the Rust Ecosystem agent (Agent 4) is essential for finding established safe abstraction patterns.
• Research quality depends on search query quality. The agents will try multiple queries but the problem statement should include domain-specific terminology to improve results.

Converted and distributed by TomeVault — claim your Tome and manage your conversions.