# Deep Research > Conducts comprehensive multi-source research on a topic - clarifies scope, plans research angles, spawns parallel analyst subagents to study each source in depth, and synthesizes findings into cited documentation. Use when the user wants thorough research, a literature review, a competitive scan, or says "deep research", "research this properly", "build me a research doc". - Skill: `sawyer-middeleer/deep-research` (Agent Skill, multi-file: 3 files) - Install (CLI): `npx skillmds@latest add sawyer-middeleer/deep-research` - Raw SKILL.md: https://api.skillmd.com/api/skills/sawyer-middeleer/deep-research/raw - Safety review: pending - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: Docs & Writing - Author: Sawyer-Middeleer (https://skillmd.com/u/sawyer-middeleer) - Updated: 2026-09-10 - Page: https://skillmd.com/skills/sawyer-middeleer/deep-research --- # Deep Research Systematic research workflow: clarify → plan → parallel source analysis → thematic synthesis. Deliverables are files (`plan.md`, `summaries/`, `synthesis.md`), not a chat reply — research that lands somewhere reusable. ## Phase 0: Topic `$ARGUMENTS` is the topic. If empty, ask: "What topic or research question would you like to investigate?" ## Phase 1: Clarification Use **AskUserQuestion** to set parameters — but **only ask what `$ARGUMENTS` and the conversation haven't already answered.** A well-specified request ("a deep competitive scan of X across academic and practitioner sources, ~15 sources, saved to ./research") may answer all of these; in that case skip straight to Phase 2 and confirm your read-back in one line rather than running the dialog. Batch any genuinely open questions into a single AskUserQuestion call, including the save location (question 5): 1. **Research purpose** — what is the goal; which angles matter? Suggest options contextually. (multiSelect) 2. **Scope boundaries** — inclusions, exclusions, constraints? Suggest options contextually. (multiSelect) 3. **Source preferences** (multiSelect): academic / official documentation and whitepapers / expert blogs / practitioner discussions (Reddit, X, HN, LinkedIn) / company case studies 4. **Depth** (single select): Light 6–8 sources · Medium 9–14 · Deep 15+ 5. **Save location** — where the research folder goes (default: ask, or use a knowledge base's research location if one is detected) ## Phase 2: Plan & Approve **Brief preliminary scan:** search for 2–3 representative sources; identify major themes, terminology, key authors; note unexpected angles worth folding in. **Create the plan** from `${CLAUDE_PLUGIN_ROOT}/skills/deep-research/templates/research-plan.md`: 1. Create `//` at the save location from Phase 1 2. Save the plan to `/plan.md` with: 3–5 research angles, source strategy per the user's preferences, synthesis approach (thematic / comparative / chronological), expected deliverables, known challenges 3. Get the user's approval before executing — pivoting mid-research isn't supported, so the plan carries the weight **Knowledge-base check:** only treat the location as a knowledge base if there's a positive signal it manages *notes* — a `conventions.md` describing note frontmatter/tags/links, or a CLAUDE.md with a "knowledge base"/notes-conventions section. A bare `CLAUDE.md` (the norm in code repos) is **not** a knowledge base — don't infer note conventions from it. When a real KB is detected, adopt its frontmatter, tag, and link conventions for every file this workflow writes, and use its research location if it names one. ## Phase 3: Execute ### Setup 1. Create `/synthesis.md` from `${CLAUDE_PLUGIN_ROOT}/skills/deep-research/templates/research-synthesis.md` 2. Create `/summaries/` ### Queries → validated URLs 1. For each research angle, derive 2–4 specific search queries (total = target source count) 2. WebSearch each query; pick the strongest result 3. **Validate every URL with a minimal WebFetch** ("extract the title and first paragraph") before spawning any analyst. Treat as inaccessible: dead links, and **paywalled pages** — if the fetch returns only a teaser, an abstract, or a login/subscribe wall instead of the substance, the analyst will get the same, so don't send it. Replace with an alternate, but **cap at ~2 alternates per query**; if none are accessible, drop that query and note the gap rather than looping indefinitely. 4. Record which angle each validated URL serves, and which queries ended with no accessible source **Source quality bar — include only if:** unique insight or data · authoritative voice · contrarian/edge perspective worth representing · primary research or original analysis. ### Spawn analysts in parallel **One message, N subagent-spawn calls (the Agent tool, historically "Task")** — all analysts run simultaneously: ``` subagent_type: "deep-research:research-analyst" description: "Research " prompt: "Source URL: Research focus: Research purpose: Working directory: / Analyze this source per your instructions and save your summary to //summaries/.md, then report your key insights." ``` Wait for all analysts to complete. ### Reconcile before synthesizing Don't trust the analysts' self-reported success. After they finish: 1. List `summaries/` and match files against the set of URLs/angles you spawned 2. For any analyst that saved nothing (or to the wrong path), **re-spawn it once** 3. If it fails again, record the source as a permanent gap — name it in `synthesis.md`'s limitations and in the Phase 4 report; don't silently shrink the research 4. Only proceed once every spawned source is either reconciled or recorded as a gap ### Synthesize 1. Read every summary in `summaries/` 2. Organize **by theme, not by source** — each theme section integrates insights across sources 3. Per theme: core findings with citations to summary files · evidence and examples · consensus · contradictions and debates · practical implications · open questions 4. Conclusions proportional to evidence — claims need multiple sources; note confidence and source quality 5. Executive summary last: key findings across themes, limitations of the research Cite summaries liberally — use the knowledge base's link style if one was detected, otherwise relative markdown links (`[title](summaries/filename.md)`), which resolve in any markdown viewer (a bare `[[wikilink]]` only resolves inside Obsidian-style tools). **Sources Consulted** — end `synthesis.md` with a bibliography: every source as `[title](original-url)` with its publication date where known, grouped by research angle, plus the recorded gaps. This is the shareable citation trail; local summary links alone are useless to anyone you send the doc to. ### Verify before finalizing A structural synthesis isn't a verified one. Before delivering: - Spot-check the highest-stakes claims (the ones a decision would rest on) against the original sources, not just the summaries — flag any the sources don't actually support - Note where the evidence is thin or single-sourced rather than stating it with the same confidence as well-supported findings - Run one gap pass: which planned angles ended up under-covered, and say so ### Quality review - [ ] Every research angle **from `plan.md`** is represented or its gap is noted (check against the plan, not just against the summaries that exist) - [ ] Organized thematically, not source-by-source - [ ] Findings cite source summaries; contradictions identified and explained - [ ] Conclusions proportional to evidence strength; thin/single-source claims marked - [ ] Sources Consulted bibliography present with working original URLs - [ ] Internal links resolve; frontmatter complete (per KB conventions if detected) ## Phase 4: Deliver Report to the user: - Where everything lives (`plan.md`, `synthesis.md`, `summaries/`) - Major findings and themes, briefly - Limitations: inaccessible sources, thin coverage, lower-quality evidence - Anything unexpected or particularly significant ``` // ├── plan.md ├── synthesis.md └── summaries/ ├── .md └── .md ```