kyzooghost/llm-wiki

LLM Wiki

A pattern for building a personal knowledge wiki that the LLM maintains incrementally, instead of re-deriving knowledge from raw sources on every query.

Core idea

Three layers:

• Raw sources (raw/) - immutable, user-curated. Articles, papers, transcripts, journal entries. The LLM reads but never modifies.
• Wiki (wiki/) - LLM-owned markdown pages. Summaries, entity pages, concept pages, analyses, an index, a log.
• Schema (AGENTS.md at the wiki root) - per-wiki conventions and workflows. Co-evolved with the user. Tells any LLM working in the wiki how to behave.

The wiki is a compounding artifact. Every ingest enriches it. Every query can be filed back into it. Cross-references, contradictions, and synthesis already live there - the LLM doesn't rebuild them on each turn.

The user curates sources, asks questions, and directs analysis. The LLM does the bookkeeping: summarizing, cross-referencing, filing, updating. Humans abandon wikis because maintenance grows faster than value. LLMs don't.

Routing

Match the user's invocation to one of four operations:

| Trigger phrases | Operation | Section | | --- | --- | --- | | /wiki-init, "set up a wiki for X", "form a wiki", "bootstrap a wiki" | Bootstrap | Operation: Bootstrap | | /wiki-ingest, "ingest this source", "add this to my wiki", "process this article into the wiki" | Ingest | Operation: Ingest | | /wiki-query, "query my wiki", "ask my wiki", "what does my wiki say about X" | Query | Operation: Query | | /wiki-lint, "lint my wiki", "health-check my wiki", "audit my wiki" | Lint | Operation: Lint |

For Ingest/Query/Lint: if the current directory has no wiki (no AGENTS.md + wiki/ + raw/), ask the user for the wiki path or offer to bootstrap one.

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Conventions (shared core)

Every operation follows these rules. They are intentionally portable: plain markdown, no editor- or plugin-specific syntax.

Directory layout

<wiki-root>/
  AGENTS.md          # schema/conventions for THIS wiki, co-evolved with user
  raw/               # immutable user-curated sources
    assets/          # downloaded images and binary assets (optional)
  wiki/              # LLM-owned markdown pages
    index.md         # content-oriented catalog
    log.md           # chronological append-only record
    <pages>.md

Linking

• Standard markdown only. [Gandalf](gandalf.md). Never [[Gandalf]].
• Links between wiki pages are relative paths within wiki/.
• Citations to raw sources use relative paths to raw/ from the wiki page (e.g. [Article](../raw/some-article.md)).
• This is the single biggest portability rule: it works in VS Code, Cursor, Obsidian, GitHub web, and plain text editors.

Filenames

• Kebab-case: gandalf.md, the-shire.md, meeting-2026-04-15.md.
• No spaces, no capital letters, no [[brackets]].

Frontmatter

Optional. If a wiki uses YAML frontmatter (e.g. tags, source_count, updated), the wiki's AGENTS.md defines the schema. The skill never requires it.

index.md format

Content-oriented catalog. Flat lists grouped by category. Categories typical for most wikis:

# Index

## Entities
- [Gandalf](gandalf.md) - Maiar wizard, member of the Istari.
- [The Shire](the-shire.md) - Hobbit homeland in Eriador.

## Concepts
- [The One Ring](one-ring.md) - Sauron's master ring of power.

## Sources
- [The Fellowship of the Ring](fellowship-summary.md) - 2026-04-15.

## Analyses
- [Comparative power of the Maiar](analysis-maiar-power.md) - 2026-04-20.

Each entry: - [Title](path.md) - one-line summary. Update on every ingest and every filed-back query.

log.md format

Append-only, chronological. Every entry starts with a parseable prefix:

## [2026-04-15] ingest | The Fellowship of the Ring (chapters 1-3)
- New: [fellowship-summary.md](fellowship-summary.md), [bilbo.md](bilbo.md)
- Updated: [gandalf.md](gandalf.md), [the-shire.md](the-shire.md), [index.md](index.md)

## [2026-04-20] query | How does the Ring corrupt its bearers?
- Filed: [analysis-ring-corruption.md](analysis-ring-corruption.md)
- Read: [one-ring.md](one-ring.md), [bilbo.md](bilbo.md), [frodo.md](frodo.md), [gollum.md](gollum.md)

## [2026-04-25] lint | health check
- 2 orphan pages, 1 broken link, 3 missing cross-references suggested

The ## [YYYY-MM-DD] {op} | {title} prefix lets the user run grep '^## \[' wiki/log.md | tail -10 to skim recent activity.

Page types

Most wikis settle on four page types. The AGENTS.md template encodes them but they are not strict.

• Entity - a person, place, organization, character, etc. Has properties, relationships, references.
• Concept - an idea, theme, mechanism, framework. Has definition, examples, contrasts.
• Source summary - the LLM's summary of a single raw source, with citations back into raw/.
• Analysis - a synthesis or comparison generated from a query, filed back into the wiki.

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Operation: Bootstrap

Trigger: /wiki-init, or natural-language equivalents.

Phase 1 - Discovery (single consolidated prompt)

Ask the user, in one message:

1. Subject area - one short phrase that names what this wiki is about. Examples: "Tolkien legendarium", "personal psychology and goals", "competitor X due diligence", "GraphQL deep-dive".
2. Target path - absolute or relative path where the wiki should live. Default: current working directory. If non-empty and not already a wiki, ask for confirmation.
3. Source types - what kinds of inputs they expect to feed in. Examples: articles, papers, podcast transcripts, journal entries, meeting notes, books, mixed.
4. Output formats - markdown only, or also slide decks (Marp), charts, comparison tables, canvases.
5. Frontmatter preference - none (default), or YAML frontmatter with a small schema (e.g. tags, source_count, updated).

Do not proceed until all five are answered.

Phase 2 - Scaffold

Create the directory structure exactly as documented under Conventions: Directory layout:

• <wiki-root>/raw/
• <wiki-root>/raw/assets/
• <wiki-root>/wiki/
• <wiki-root>/wiki/index.md - empty catalog stub with the four category headers (Entities, Concepts, Sources, Analyses)
• <wiki-root>/wiki/log.md - one bootstrap entry: ## [{today}] bootstrap | {subject_area}
• <wiki-root>/AGENTS.md - read references/agents-template.md, substitute the placeholders below, write the result.

Placeholders to substitute in the template:

| Placeholder | Source | | --- | --- | | {SUBJECT_AREA} | Phase 1 answer 1 | | {SOURCE_TYPES} | Phase 1 answer 3 | | {OUTPUT_FORMATS} | Phase 1 answer 4 | | {FRONTMATTER_CHOICE} | Phase 1 answer 5 (literal text describing the choice) | | {BOOTSTRAP_DATE} | Today's date in YYYY-MM-DD format |

If a Phase 1 answer is vague, leave the placeholder filled with the user's literal phrasing - the user can refine AGENTS.md later.

Phase 3 - Confirm

Print the resulting tree (depth 2, leaves only) and tell the user:

• The wiki path
• The next concrete step: /wiki-ingest <source-path> to file the first source
• That AGENTS.md is meant to be edited as conventions emerge

Do not ingest anything during bootstrap. Bootstrap is structural only.

---

Operation: Ingest

Trigger: /wiki-ingest <source>, or natural-language equivalents.

Phase 1 - Locate the source

Source can be:

• A path (file in raw/ or anywhere on disk - copy into raw/ if it isn't already there)
• A URL (fetch and convert to markdown, save to raw/)
• Pasted content (write to a new file in raw/ with a kebab-case name from a 2-4 word summary)

If the source already exists in raw/, do not overwrite. Ask for confirmation if the user re-ingests.

Phase 2 - Read and discuss

Read the source. Surface 3-7 key takeaways to the user. Ask:

• Which takeaways to emphasize in the wiki
• Whether any contradict claims already in the wiki (read wiki/index.md first to know what's there)
• Whether to create new entity/concept pages, or fold the source into existing ones

Do not write to the wiki yet. Ingest is a discussion, not a dump. The source prompt this skill is based on emphasizes: "I prefer to ingest sources one at a time and stay involved."

Phase 3 - Write the summary page

Create wiki/<source-slug>.md with:

• Title (from source title)
• Citation block linking back to raw/<source-file>
• Sections for the takeaways the user emphasized
• Inline links to entity/concept pages mentioned, even if those pages do not exist yet (so they show up as broken links and surface in lint)

Phase 4 - Update affected pages

A single source typically touches 10-15 wiki pages. This phase is non-optional.

For each entity, concept, or claim mentioned in the source:

1. Check wiki/index.md - does a page already exist?
2. If yes: read it, surgically integrate the new information. Note when the source contradicts existing claims (do not silently overwrite - flag the contradiction in the page itself with a > NOTE: ... blockquote).
3. If no, and the user emphasized this entity/concept in Phase 2: create the page.

Cross-reference: every page that mentions another page must link to it.

Phase 5 - Update index.md

Add new pages under their categories. Refresh the one-line summaries of any pages whose scope changed.

Phase 6 - Append to log.md

## [{today}] ingest | {Source Title}
- New: [page-1](page-1.md), [page-2](page-2.md)
- Updated: [page-3](page-3.md), [page-4](page-4.md), [index.md](index.md)
- Contradictions: 0 (or list)

Phase 7 - Confirm

Show the user the list of files created and modified, and a short summary of contradictions/uncertainties surfaced.

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Operation: Query

Trigger: /wiki-query <question>, or natural-language phrasings.

Phase 1 - Read index.md

Read wiki/index.md first. It is a content-oriented catalog and is the cheapest way to find candidate pages at small/medium scale. No embedding RAG is required.

If the wiki has grown beyond what index.md can serve well (typically hundreds of pages), the wiki's AGENTS.md may declare a search tool to use instead. Defer to it.

Phase 2 - Read candidate pages

Identify 3-10 pages relevant to the question and read them with the Read tool. Read linked pages transitively when needed.

If the answer requires raw-source detail not captured in the wiki summary, follow the citation back into raw/ and read there too.

Phase 3 - Synthesize with citations

Produce the answer in the format that fits the question:

• Default: a markdown response with inline links back to the wiki pages used
• Comparison: a markdown table
• Slide deck: a Marp markdown document
• Chart: a matplotlib script
• Canvas: when the answer is data-heavy or warrants rich layout

Citations are wiki page links ([Gandalf](wiki/gandalf.md)), with raw-source links secondary.

Phase 4 - Offer to file the answer back

Good answers are valuable artifacts. Ask the user: "File this back into the wiki as an analysis page?"

If yes:

1. Write to wiki/analysis-<short-slug>.md
2. Add an entry under ## Analyses in wiki/index.md
3. Append a log entry: ## [{today}] query | {Question} with new/read pages listed

If no, leave the wiki unchanged. The answer lives in the chat only.

---

Operation: Lint

Trigger: /wiki-lint, or natural-language equivalents.

Read-only. Do not auto-fix. Report findings, ranked by severity.

Checks

1. HIGH - Broken links - markdown links in wiki/*.md that point to a missing file or missing heading. Use the same approach as commands/audit-docs.md Check 7.
2. HIGH - Contradictions - claims on different pages that conflict. Cross-reference pages that mention the same entity/concept and look for > NOTE: blockquotes left during ingest, or for direct contradictions in prose.
3. MEDIUM - Stale claims - pages whose claims are superseded by newer source summaries. Cross-reference the log to see ingest order.
4. MEDIUM - Missing pages - concepts mentioned >=3 times across the wiki but lacking their own page.
5. LOW - Orphan pages - pages with zero inbound links from any other wiki page (excluding index.md and log.md).
6. LOW - Missing cross-references - page A mentions entity B (which has its own page), but A does not link to B.
7. LOW - Data gaps - topics where the wiki is thin and the user could profitably search the web or seek another source.

Report format

Mirror commands/audit-docs.md:

## Wiki Lint: {N} issues found across {M} pages

### [HIGH] Broken link: {brief title}
- **Location:** wiki/gandalf.md:42 - links to `mithrandir.md`
- **Problem:** target file does not exist
- **Suggested fix:** {actionable recommendation}

### [MEDIUM] Missing page: {brief title}
- **Mentioned in:** wiki/the-shire.md:12, wiki/bilbo.md:8, wiki/frodo.md:23
- **Suggested fix:** create `wiki/sting.md` for the recurring entity

### [LOW] Orphan: wiki/old-notes.md
- No inbound links from any other wiki page.
- **Suggested fix:** link from a relevant page or remove.

After all findings, print [OK] lines for clean checks. Append a log entry summarizing the lint:

## [{today}] lint | health check
- {N} HIGH, {M} MEDIUM, {L} LOW

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Portability and Obsidian decoupling

This skill produces wikis that work without Obsidian. The defaults below are non-negotiable:

• No [[wikilinks]] - standard markdown links only
• No required Obsidian plugins (Dataview, Marp, Web Clipper)
• No LLM-specific schema filename (we use AGENTS.md, which Claude, Codex, Cursor, and other agents all read)
• No required attachment-folder configuration
• No tags:: or other Obsidian-only frontmatter syntax

Optional integrations

If the user happens to use one of these viewers, the wiki layers cleanly on top:

• Obsidian - graph view works on standard markdown links. The user can opt into wikilinks afterward but the skill does not produce them.
• VS Code / Cursor - markdown preview and "go to file" navigation work natively.
• GitHub web - the wiki renders directly when pushed to a repo.
• Dataview (Obsidian) - if the wiki opted into YAML frontmatter during bootstrap, Dataview queries work over it.
• Marp - if "slide decks" was selected in bootstrap output formats, the query operation can produce Marp-compatible markdown.

The wiki is a git repo of markdown files. Version history, branching, diffs, and collaboration come for free.

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Ground rules

• Read-only on raw/. The LLM never modifies sources. Treat the directory as immutable.
• The LLM owns wiki/. The user reads it; the LLM writes it. The user can edit too, but the skill assumes LLM authorship.
• The user owns AGENTS.md. The skill seeds it during bootstrap; afterward both user and LLM co-evolve it.
• One source at a time, by default. Ingest is conversational. Batch ingestion is possible but the user must opt in explicitly.
• Cite everything. Every claim in the wiki should trace to a source summary or another wiki page. Lint catches drift.
• Surface contradictions, do not hide them. Use > NOTE: blockquotes during ingest. Lint elevates them.
• No silent overwrites. When new information conflicts with old, ask before replacing.