LLM Wiki#

Build and maintain a persistent, compounding knowledge base of interlinked markdown files. The LLM writes and maintains the wiki. The human curates sources, asks questions, and guides the analysis.

This is not RAG. Instead of re-deriving knowledge at query time, the LLM incrementally builds a structured wiki that grows richer with every source added and every question asked. Cross-references are pre-built. Contradictions are already flagged. Synthesis already reflects everything ingested.

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First run — bootstrap#

If wiki/index.md does not exist, the wiki is uninitialized. Ask the user:

1. What is this wiki for? (domain, topic, purpose)
2. Where is the root directory? (defaults to current working directory)
3. What kinds of sources will you add? (articles, PDFs, transcripts, notes…)
4. How hands-on do you want to be during ingest? (discuss first vs. batch silently)

Then:

1. Create raw/ and wiki/ directories.
2. Create wiki/index.md with a # Wiki Index heading and empty page sections.
3. Create wiki/log.md with a # Log heading.
4. Confirm the setup to the user and show them the directory layout.

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Directory structure#

text

{root}/
  raw/          -- source documents (immutable — never modify)
  wiki/
    index.md    -- table of contents: every page with a one-line summary
    log.md      -- append-only chronological record of all operations
    *.md        -- generated pages (summaries, entities, concepts, etc.)

raw/ is the user's domain. The LLM owns everything under wiki/.

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Ingest#

When the user adds a source to raw/ and asks you to process it:

1. Read the full source. Never modify anything in raw/.
2. Discuss key takeaways with the user before writing anything.
3. Create a summary page at wiki/{source-name}.md.
4. Create or update concept, entity, and topic pages for every major idea or entity the source touches. A single source typically touches 5–15 pages. That is normal.
5. Add [[wiki-links]] throughout every page you create or update. Links are the primary value of the wiki — connect aggressively.
6. Note contradictions. If new information disagrees with an existing claim, flag it on both pages: (contradicts: [[other-page]])
7. Update wiki/index.md: add new pages with one-line descriptions, keep sorted.
8. Append to wiki/log.md: date, source name, pages created, pages updated.

Do not write wiki pages before completing step 2.

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Query#

When the user asks a question:

1. Read wiki/index.md first to find relevant pages.
2. Read those pages and synthesize an answer.
3. Cite specific wiki pages in your response.
4. If the answer is not in the wiki, say so clearly.
5. If the answer is valuable, offer to save it as a new wiki page.

Good answers should be filed back into the wiki so they compound over time. A comparison you generated, an analysis, a connection the user discovered — these are valuable and should not disappear into chat history.

Output formats — answers can take different forms depending on the question:

• Markdown page (default)
• Comparison table
• Marp slide deck (if the user has Marp)
• Matplotlib chart (for numeric data)
• Any format the user requests

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Lint / audit#

When the user asks you to lint or audit the wiki:

• Contradictions — claims on different pages that disagree.
• Orphan pages — pages with no inbound [[links]] from other pages.
• Missing pages — concepts referenced in links that have no corresponding file.
• Stale claims — facts that newer sources have superseded.
• Format violations — pages that do not follow templates/page.md.
• Missing citations — factual claims with no (source: ...) reference.
• Data gaps — concepts that are mentioned but thin; suggest new sources to find.

Report findings as a numbered list, each with a suggested fix. Offer to apply fixes.

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Index format ( wiki/index.md)#

markdown

# Wiki Index

## Summary pages
- [[source-name]] — one-line description

## Entity pages
- [[entity-name]] — one-line description

## Concept pages
- [[concept-name]] — one-line description

Keep entries sorted within each section.

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Log format ( wiki/log.md)#

Append one block per operation. Never edit existing entries.

markdown

## [YYYY-MM-DD] ingest | Source Title

- Created: [[page-a]], [[page-b]]
- Updated: [[page-c]], [[page-d]]
- Notes: any notable contradictions, gaps, or decisions

The ## [YYYY-MM-DD] prefix makes the log greppable: grep "^## \[" wiki/log.md | tail -5

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Page format#

Follow templates/page.md. Every page must have:

markdown

# Page Title

**Summary**: One to two sentences.

**Sources**: Raw source files this page draws from.

**Last updated**: YYYY-MM-DD

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Content with [[wiki-links]] throughout.

## Related pages

- [[page]]

• File names: lowercase, hyphens, .md (e.g. machine-learning.md)
• Every factual claim: (source: filename.ext)
• Contradictions: (contradicts: [[page-name]])
• Unsourced claims: (needs verification)

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Optional tooling#

These are not required but mentioned in case the user wants them:

ToolPurposeqmdLocal search over wiki pages — BM25/vector hybrid, MCP server + CLIObsidianMarkdown editor with graph view, backlinks, Dataview, Marp pluginObsidian Web ClipperBrowser extension to clip articles to markdownMarpMarkdown → slide decks; useful for presenting wiki synthesisDataviewObsidian plugin — queries over YAML frontmatter in wiki pagesgitVersion history and branching for the wiki directory

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Rules#

• Never modify anything in raw/.
• Always update wiki/index.md and wiki/log.md after every change.
• When uncertain how to categorize something, ask the user before writing.
• Write in plain language. The wiki is for the user, not for demonstration.
• Do not create wiki pages for things that belong in raw/ (raw sources stay raw).
• Links are the primary value. Connect aggressively. A page with no outbound links is a missed opportunity.