Wiki Research — Autonomous Multi-Round Research

You are running an autonomous research loop on a topic, synthesizing what you find, and filing the results into the Obsidian wiki as permanent knowledge.

Before You Start

1. Resolve config — follow the Config Resolution Protocol in llm-wiki/SKILL.md (inline @name override → walk up CWD for .env → ~/.llm-wiki/config → prompt setup). This gives OBSIDIAN_VAULT_PATH and OBSIDIAN_LINK_FORMAT (default: wikilink).
2. Read $OBSIDIAN_VAULT_PATH/index.md to understand what's already in the wiki — don't re-research things the wiki covers well
3. Read $OBSIDIAN_VAULT_PATH/hot.md if it exists — it surfaces recent context
4. Check $OBSIDIAN_VAULT_PATH/_meta/research-config.md if it exists (older vaults keep it at references/research-config.md) — it may define source preferences, domains to skip, or confidence rules for this vault
5. Read the CATEGORIES table in AGENTS.md (or run llm-wiki layout --json). The output below goes to the folders holding the reference, concept, entity and synthesis roles — references/, concepts/, entities/ and synthesis/ in a standard vault; any role no row claims falls to the catch-all row.

When writing internal links in generated pages, apply the link format from llm-wiki/SKILL.md (Link Format section) using the OBSIDIAN_LINK_FORMAT value.

Confirm the research topic with the user if it's ambiguous. Then proceed.

Research Configuration (optional)

If _meta/research-config.md (or the older references/research-config.md) exists in the vault, read it and apply any rules it defines:

• Source preferences (e.g., prefer academic sources, avoid certain domains)
• Domains to skip
• Confidence scoring adjustments
• Topic-specific constraints

If the file doesn't exist, proceed with defaults.

Round 1 — Broad Survey

Goal: Get a wide map of the topic.

1. Decompose the topic into 3-5 distinct angles (e.g., for "vector databases": what they are, when to use them, leading implementations, trade-offs, production gotchas)
2. For each angle, run 2-3 WebSearch queries using varied phrasing
3. For the top 2-3 results per angle, use WebFetch (or defuddle <url> if available — cleaner extraction) to get content
4. From each fetched page, extract:
   • Key claims — what the source explicitly states
   • Concepts — ideas, terms, frameworks introduced
   • Entities — tools, people, organizations mentioned
   • Contradictions — places where sources disagree with each other

Track what's covered and what's missing as you go.

Round 2 — Gap Fill

Goal: Close the holes left by Round 1.

Review what Round 1 produced:

• What questions did sources raise but not answer?
• Where do sources contradict each other?
• Which angles got thin coverage?

Run up to 5 targeted searches specifically addressing these gaps. Prefer primary sources, official documentation, and authoritative analyses over link aggregators.

Add findings to your working set. Update the contradiction list.

Round 3 — Synthesis Check

Goal: Resolve contradictions; confirm depth is sufficient.

If major contradictions remain unresolved:

• Run one final targeted pass (2-3 searches) to find authoritative resolution
• If resolution is impossible, flag the contradiction explicitly in the synthesis page

If contradictions are minor or the topic feels well-covered after Round 2, skip additional searching and proceed to filing.

Halt condition: Stop when depth is achieved or 3 rounds are complete — do not loop indefinitely.

Filing — Write Wiki Pages

Organize all findings into wiki pages across four output areas:

1. The reference folder — one page per major source

For each significant source (typically 4-8 pages total):

---
title: >-
  <Source title>
category: references   # the folder you wrote it to (in a single-folder vault: references)
tags: [<2-4 domain tags>]
sources:
  - "<URL>"
source_url: "<URL>"
created: <ISO-8601 timestamp>
updated: <ISO-8601 timestamp>
summary: >-
  <1-2 sentences describing what this source covers, ≤200 chars>
provenance:
  extracted: 0.X
  inferred: 0.X
  ambiguous: 0.X
base_confidence: <0.17 + 0.5 × classify(url) for a single source>
lifecycle: draft
lifecycle_changed: <ISO date today>
---

Body: title, URL, what it covers, key claims (with provenance markers), limitations.

2. The concept folder — one page per substantive concept

For each significant concept surfaced across sources:

Standard concept frontmatter + body. Link concepts to each other and to source pages.

3. The entity folder — tools, organizations, people

For each significant entity encountered (tools, libraries, companies, key authors):

Standard entity frontmatter. Link back to concepts that use the entity and sources where it appears.

4. <synthesis folder>/Research: [Topic].md — Master synthesis

The primary output: a structured synthesis of everything found.

---
title: >-
  Research: <Topic>
category: synthesis   # the folder you wrote it to (in a single-folder vault: synthesis)
tags: [<3-5 domain tags>, research]
sources: [<list of source URLs or page paths>]
created: <ISO-8601 timestamp>
updated: <ISO-8601 timestamp>
summary: >-
  Synthesis of <N>-round research on <topic>. Covers <core findings in ≤200 chars>.
provenance:
  extracted: 0.X
  inferred: 0.X
  ambiguous: 0.X
base_confidence: <min(N_unique_sources/3,1.0)×0.5 + avg_source_quality×0.5>
lifecycle: draft
lifecycle_changed: <ISO date today>
---

# Research: <Topic>

## Overview
<2-4 sentence executive summary of what the research found>

## Key Findings
<Bulleted list of the most important claims, each with a [[source page]] citation>

## Core Concepts
<Links to concept pages created, with one-line descriptions>

## Entities & Tools
<Links to entity pages, with one-line descriptions>

## Contradictions & Open Questions
<Where sources disagree or where the research hit limits>

## Sources Consulted
<Linked list of all source pages>

Cross-linking

After filing all pages:

• Every concept page should link to at least 2 source pages
• Every source page should link to the concept pages it informed
• The synthesis page should link to all concept, entity, and source pages produced

Check index.md for existing pages on the same topics — merge into existing pages rather than creating duplicates.

Update Tracking Files

.manifest.json — Add a research entry:

{
  "type": "research",
  "topic": "<topic>",
  "researched_at": "TIMESTAMP",
  "rounds_completed": 3,
  "sources_fetched": N,
  "pages_created": ["..."],
  "pages_updated": ["..."]
}

index.md — Add all new pages under their respective sections.

log.md — Append:

- [TIMESTAMP] WIKI_RESEARCH topic="<topic>" rounds=N sources_fetched=N pages_created=M

hot.md — Update Recent Activity with the research topic and core finding. Update Active Threads if this is ongoing. Update updated timestamp.

Quality Checklist

• 3 rounds completed (or halted at sufficient depth)
• Synthesis page exists at <synthesis folder>/Research: [Topic].md
• Source pages written for major references
• Concept and entity pages written for significant items
• Contradictions flagged in synthesis page
• All pages cross-linked
• index.md, log.md, hot.md, .manifest.json updated

QMD Refresh After Vault Writes

GUARD: If $QMD_WIKI_COLLECTION is unset — the default — skip this step. QMD is a search index, not the source of truth.

When it is set, read llm-wiki/references/qmd.md and follow the Refresh section after this skill has written vault markdown. If refresh fails, do not roll back the vault changes; report the QMD status separately.