Obsidian-vault-agent deep-research

<Purpose> Iterative, multi-perspective research that explores broadly and goes deep. Unlike `/research` (single-pass, web-only, 5-10 sources), this skill: - Discovers PERSPECTIVES before searching (not just sub-questions) - Searches 4 source types in parallel: web, academic papers, Reddit, vault - Runs an exploration → critique loop that finds gaps, contradictions, and new angles - Uses an outline-first approach to prevent hallucination - Produces a note with fact-level citations, a confidence map, and explicit uncertainty

The architecture is inspired by Stanford's STORM (perspective discovery + outline-first), Anthropic's multi-agent research system (parallel exploration + intelligent critique), and pi-autoresearch (living state files that survive context resets). </Purpose>

<Use_When>

• User wants DEEP understanding, not a quick summary
• Topic is complex, contested, or multi-faceted
• User needs to make a decision based on the research
• User wants to compare competing approaches with evidence
• User explicitly asks for /deep-research or "thorough research" </Use_When>

<Do_Not_Use_When>

• User wants a quick answer (use /research instead)
• User wants to find academic papers specifically (use /paper-discover)
• User wants to process an existing vault note (use /process)
• User wants cross-domain vault synthesis (use /synthesize) </Do_Not_Use_When>

<Steps>

Stage 0: SETUP

Parse

$ARGUMENTS

for the topic and optional depth flag:

• --quick

  : faster, fewer rounds, sonnet everywhere, no perspective discovery

• --deep

  : more rounds, opus for critic and synthesis, outline reviewed by user
• Default (no flag): balanced — perspective discovery, 2-4 rounds, opus for synthesis

Create the workspace:

TOPIC_SLUG=$(echo "$TOPIC" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/-/g' | sed 's/--*/-/g' | cut -c1-30)
WORK_DIR="temp/research-${TOPIC_SLUG}"
mkdir -p "$WORK_DIR"/{findings,gaps}

Resume check: Before creating, check if the workspace already exists:

ls "$WORK_DIR/state.md" 2>/dev/null

If

state.md

exists, read it and ask the user: "Found incomplete research on [topic] (round N). Resume or start fresh?" If resuming, read

state.md

to determine which stage to skip to.

Tell the user what's happening:

Deep researching "{topic}" ({depth mode}).
Setting up workspace at {WORK_DIR}...

Stage 1: PLAN — Decompose + Discover Perspectives

Read the agent definition:

Read(".claude/skills/deep-research/agents/research-planner.md")

Launch the planner agent:

Agent(
  model="sonnet",
  prompt="You are Research Planner. Follow these instructions exactly:

  [INSERT FULL CONTENT OF agents/research-planner.md HERE]

  TOPIC: {topic}
  DEPTH_MODE: {quick|standard|deep}
  WORK_DIR: {WORK_DIR}

  Write state.md and ideas.md to the WORK_DIR."
)

After the planner completes, read

state.md

briefly and tell the user:

Perspectives identified: {list}
Sub-questions: {count}
Exploration ideas: {count}
Starting exploration...

Stage 2: EXPLORE — Parallel Deep Dives

Read the agent definition and source tiers reference:

Read(".claude/skills/deep-research/agents/research-explorer.md")
Read(".claude/skills/deep-research/references/source-tiers.md")

Read

ideas.md

and pick the 3-5 highest-priority unexplored ideas.

For EACH selected idea, launch an explorer agent in the background:

Agent(
  model="sonnet",
  run_in_background=true,
  prompt="You are Research Explorer. Follow these instructions exactly:

  [INSERT FULL CONTENT OF agents/research-explorer.md HERE]

  SOURCE TIERS REFERENCE:
  [INSERT FULL CONTENT OF references/source-tiers.md HERE]

  ANGLE: {the idea to explore}
  PERSPECTIVE: {which perspective this serves}
  QUERIES: {the search queries from ideas.md}
  STATE_CONTEXT: {summary from state.md — what's already known}
  OUTPUT_FILE: {WORK_DIR}/findings/angle-{NN}-{slug}.md

  Write your findings to OUTPUT_FILE using the Write tool."
)

Wait for all explorer agents to complete. Verify each output file exists:

ls {WORK_DIR}/findings/

Update

ideas.md

— mark explored ideas as

[x]

. If explorers discovered new threads, append them to ideas.md under "## Discovered During Research".

Tell the user:

Round {N} complete: explored {count} angles, found {count} sources.
Running critique...

Stage 3: CRITIQUE — The Intelligence Layer

For

--quick

mode: skip the critic agent entirely. Instead, briefly review the findings yourself — check if any sub-questions are obviously thin. If so, do ONE more targeted search round. Then proceed to Stage 5.

For standard and

--deep

mode: Launch the critic agent.

Read the agent definition:

Read(".claude/skills/deep-research/agents/research-critic.md")

Agent(
  model="opus",
  prompt="You are Research Critic. Follow these instructions exactly:

  [INSERT FULL CONTENT OF agents/research-critic.md HERE]

  WORK_DIR: {WORK_DIR}
  ROUND: {current round number}

  Read all files in the workspace, then write your critique to
  {WORK_DIR}/gaps/critique-round-{N}.md.
  Also update {WORK_DIR}/state.md with the coverage map.
  If you have new research ideas, append them to {WORK_DIR}/ideas.md."
)

Stage 4: DECIDE — Continue or Proceed

Read the critic's output:

{WORK_DIR}/gaps/critique-round-{N}.md

Check the recommendation: CONTINUE or SUFFICIENT.

If CONTINUE AND within guardrails:

• Read updated

  ideas.md

  for new angles
• Loop back to Stage 2 with the new ideas

If SUFFICIENT OR guardrails hit:

• Proceed to Stage 5

Guardrails (override critic recommendation if needed):

• Max rounds: 2 (quick), 4 (standard), 8 (deep)
• Max total source files: 15 (quick), 30 (standard), 50 (deep)
• If the latest round's explorers produced < 3 new substantive claims → stop
• Count rounds by reading how many

  critique-round-*.md

  files exist

Tell the user:

Critic says: {CONTINUE/SUFFICIENT}. {brief reason}
{If continuing: "Exploring {N} more angles..."}
{If done: "Evidence base ready. Building outline..."}

Stage 5: OUTLINE — Structure Before Content

Build an outline that maps each section to its supporting evidence. This is the STORM discipline — commit to structure before writing to prevent hallucination.

Read the final critique, all findings files, and state.md. Then write

{WORK_DIR}/outline.md

with this structure:

# Outline: {Topic}

## TL;DR
- {Key finding 1} ← supported by: angle-{NN}, angle-{NN}
- {Key finding 2} ← supported by: angle-{NN}
- {Key finding 3} ← supported by: angle-{NN}, angle-{NN}

## Section: {Theme 1 — insight as heading}
- Key point: {insight}
- Sources: angle-{NN} (claims X,Y), angle-{NN} (claim Z)
- Vault links: [[(Type) Note]] if relevant

## Section: {Theme 2 — insight heading}
- Key point: {insight}
- Sources: ...

## Section: Where Experts Disagree
- Contradiction 1: angle-{NN} vs angle-{NN} on {topic}
- Contradiction 2: ...

## Section: What's Still Uncertain
- {Gap from critic}
- {Single-source claim}

## Confidence Map Notes
- {Finding}: {confidence level} — {evidence basis}

For

--deep

mode: Show the outline to the user and wait for approval: "Here's the outline. Want me to adjust anything before I write the full note?"

For standard and

--quick

: Proceed automatically.

Stage 6: SYNTHESIZE — Write the Research Note

Read the agent definition:

Read(".claude/skills/deep-research/agents/research-synthesizer.md")

Launch the synthesizer:

Agent(
  model="opus",  # sonnet for --quick
  prompt="You are Research Synthesizer. Follow these instructions exactly:

  [INSERT FULL CONTENT OF agents/research-synthesizer.md HERE]

  WORK_DIR: {WORK_DIR}
  OUTPUT_FILE: {WORK_DIR}/synthesis.md

  Read outline.md, all findings files, all gap files, and state.md.
  Write the complete vault note body to OUTPUT_FILE.
  Do NOT include frontmatter — just the note content starting with # title."
)

Stage 7: INTEGRATE — Create Vault Note

1. Read

   {WORK_DIR}/synthesis.md

2. Generate timestamp:

   date +%Y%m%d%H%M%S
   

3. Determine subfolder — match the topic to existing vault folders:

   • ML/AI topics →

     notes/ml/

   • Startup/business →

     notes/startup/

   • Psychology →

     notes/psychology/

   • Finance →

     notes/finance/

   • Default →

     notes/research/

4. Create the vault note using

   mcp__obsidian-vault__write_note

   or Write:

   ---
   id: {YYYYMMDDHHMMSS}
   type: note
   processing_status: processed
   created_date: {YYYY-MM-DD}
   updated_date: {YYYY-MM-DD}
   ---
   
   {synthesis.md content}
   

5. Report to user:

   Research complete! Created: {note path}
   
   - Sources: {N} web, {N} academic, {N} community, {N} vault
   - Exploration rounds: {N}
   - Contradictions found: {N}
   - Key uncertainty: {biggest gap}
   
   Suggested next steps:
   - Extract terms: {list of concepts for extraction}
   - Related research: {follow-up topics}
   - Vault connections: {notes that should link to this}
   
   Workspace at {WORK_DIR}/ — delete when done.
   

</Steps>

<Tool_Usage>

• Agent: 4 agent types — planner (sonnet), explorer (sonnet, parallel), critic (opus), synthesizer (opus)
• WebSearch: Multi-query web search within explorer agents
• WebFetch: Deep-read URLs within explorer agents
• Bash: Workspace creation, timestamp, search_papers.py execution
• Grep/Glob: Vault search within planner agent
• MCP obsidian-vault: Vault search and note creation
• MCP reddit: Community source search within explorer agents
• Read: Agent definitions, workspace files, source tiers reference
• Write: Workspace files (state, ideas, outline), vault note creation </Tool_Usage>

<Examples> <Good> User: /deep-research context engineering for AI agents 1. Setup → temp/research-context-engineering/ 2. Plan → 4 perspectives (researcher, practitioner, framework builder, skeptic), 6 sub-questions, 12 exploration ideas 3. Round 1 → 4 explorer agents, 16 sources (web + papers + Reddit) 4. Critique → "practitioner perspective is thin, contradictions on context window vs. summarization tradeoff, missing: cost analysis angle" 5. Round 2 → 3 more explorers targeting gaps, 9 new sources 6. Critique → "SUFFICIENT — good coverage, 2 genuine ongoing debates to present" 7. Outline → 5 themes + disagreements + uncertainties, all mapped to sources 8. Synthesize → 55-bullet note with 25 sources, confidence map, 4 vault connections 9. Integrate → notes/ml/(Research) Context Engineering for AI Agents.md </Good> <Bad> - Searches once and stops — no critique, no gap-filling - Creates a note that just lists what each source said - Ignores the vault — no wikilinks, no checking what already exists - All sources are web — no papers, no Reddit, no diversity - No confidence map — claims everything with equal certainty - No "Where Experts Disagree" — hides contradictions instead of presenting them - Doesn't write workspace files — can't resume if interrupted </Bad> </Examples>

<Escalation_And_Stop_Conditions>

• Topic too broad ("deep research AI"): Ask user to narrow. Suggest 2-3 specific angles.
• No results from any source: Inform user, offer to create a vault-only synthesis from existing notes.
• Mostly paywalled academic sources: Note limitation, prioritize open-access and preprints.
• Topic already deeply covered in vault: Show existing notes, ask if user wants fresh perspectives or an update.
• Explorer agent fails: Check the output file. If missing, log the failure and continue with other angles — don't block the entire research on one failed agent.
• Context getting large: The workspace files ARE the state. If context is approaching limits, the user can restart and the skill will offer to resume from the workspace. </Escalation_And_Stop_Conditions>

$ARGUMENTS