LLM Wiki Manager

A Claude Code skill for building and maintaining a personal LLM-managed wiki — a persistent, compounding knowledge base where the LLM does all the writing, cross-referencing, and bookkeeping while you curate sources and ask questions.

🇹🇷 Türkçe için README.tr.md

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Quick Start

git clone https://github.com/sametbrr/llm-wiki-manager ~/.claude/skills/llm-wiki-manager

Start a new Claude Code session in your research folder:

mkdir ~/research/my-topic && cd ~/research/my-topic && claude
> "Set up an LLM wiki here. Topic: history of nutrition science."

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Features

Instead of RAG — where the LLM rediscovers answers from raw documents on every query — this pattern has the LLM compile raw sources into a persistent, interlinked markdown wiki. Each new source enriches existing pages. Cross-references are built eagerly. Contradictions are flagged. Knowledge compounds over time.

Implements Karpathy's LLM Wiki pattern as a full Claude Code skill with 8 operating modes (including multi-wiki routing), 5 idempotent Python scripts, 8 page templates, and 11 reference documents.

Without this pattern          With this pattern
────────────────────          ──────────────────
Query 1 → re-read 50 docs     Query 1 → read compiled wiki (already synthesized)
Query 2 → re-read 50 docs     Query 2 → read updated wiki (cross-refs already there)
Query 3 → re-read 50 docs     Query 3 → read updated wiki (contradictions already flagged)

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Requirements

• Claude Code or any agentskills.io-compatible agent
• Python 3.9+ (stdlib only, for the 5 included scripts — no pip install needed)

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Installation

Option 1 — git clone (recommended)

git clone https://github.com/sametbrr/llm-wiki-manager ~/.claude/skills/llm-wiki-manager

Option 2 — GitHub CLI (requires gh CLI v2.90+)

gh skill install sametbrr/llm-wiki-manager

Option 3 — .skill file

curl -L -o llm-wiki-manager.skill \
  https://github.com/sametbrr/llm-wiki-manager/releases/latest/download/llm-wiki-manager.skill
unzip llm-wiki-manager.skill -d ~/.claude/skills/llm-wiki-manager

After installing, start a new Claude Code session. The skill loads automatically when relevant.

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Usage

The skill auto-detects which mode applies from natural language. No slash commands needed.

Modes

Mode	Trigger examples	What happens
Bootstrap	"Set up a wiki", "start a knowledge base here"	Scaffolds raw/, wiki/, CLAUDE.md from templates
Ingest	"Add this PDF to the wiki", "I just read X, file it"	Reads source → writes summary → updates entity/concept pages → indexes → logs
Query	"What does the wiki say about X?", "Compare X and Y"	Reads index → candidate pages → synthesizes answer with citations → offers to file back
Update	"Smith 2024 supersedes Keys 1980, update the wiki"	Semantic sweep across all pages → diff-before-write per page → single log entry
Lint	"Health check the wiki", "anything broken?"	Runs lint_wiki.py → auto-saves wiki/reports/lint-YYYY-MM-DD.md → auto-tracks in index and log
Schema-evolve	"We should always do X going forward"	Updates CLAUDE.md so future sessions inherit the convention
Multi-wiki	"Add this to my global wiki", "promote this page to global"	Routes between project wiki and global wiki using the External Wiki: declaration in project CLAUDE.md
Teach	"How does this pattern work?", "explain the LLM wiki idea"	Explains the pattern, compares with RAG, walks through a concrete example

Full walkthrough

# 1. Go to your research folder
mkdir ~/research/my-topic && cd ~/research/my-topic && claude

# 2. Bootstrap the wiki
> "Set up an LLM wiki here. Topic: history of nutrition science."

# 3. Drop a source
cp ~/Downloads/pollan-2008.pdf raw/

# 4. Ingest it
> "Ingest Pollan's In Defense of Food"

# 5. Ask questions
> "What does the wiki say about nutritionism?"

# 6. Health check (auto-saves dated report to wiki/reports/)
> "Lint the wiki"

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The three-layer model

your-wiki/
├── CLAUDE.md          # Schema — conventions for this wiki (co-evolved over time)
├── raw/               # YOUR layer — immutable sources you curate. LLM reads, never writes.
└── wiki/              # LLM layer — all pages written and maintained by the LLM
    ├── index.md       # Content catalog (updated on every ingest)
    ├── log.md         # Append-only operation log (greppable)
    ├── hot.md         # Hot cache — most recently ingested sources and active references
    ├── sources/       # One summary page per ingested source
    ├── entities/      # People, organizations, places, products
    ├── concepts/      # Ideas, theories, frameworks, terms
    ├── notes/         # Filed-back query answers and loose pages
    └── reports/       # Auto-generated dated lint reports (wiki/reports/lint-YYYY-MM-DD.md)

Division of labor:

You do	The LLM does
Curate sources (decide what to read)	Read sources end-to-end
Ask questions, steer direction	Write summaries, entity and concept pages
Review the wiki, follow links	Update cross-references in-place
Decide what matters	Maintain index.md and log.md
Own raw/	Flag contradictions, surface gaps

You almost never write wiki pages by hand. The LLM does the bookkeeping — that's what makes the wiki compound instead of collapse.

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Core disciplines

1. LLM owns wiki/. You own raw/. No exceptions.
2. Every operation logs to log.md via append_log.py. Greppable: grep "^## \[" log.md | tail -20
3. Every new or updated page touches index.md via update_index.py. Stale index = wiki that feels lost.
4. Cross-reference aggressively. When a source mentions an entity that already has a page, update that page. Don't leave connections implicit.
5. Cite back to raw/. Every claim is traceable to a specific source file.
6. Flag contradictions, don't overwrite. New source disagrees with old claim? Both stay, marked with their source, with a > [!warning] Sources disagree callout.
7. Schema lives in CLAUDE.md. When a convention works, write it down. The next session starts informed.

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What's inside

Scripts (Python stdlib, no dependencies, all idempotent)

Script	Purpose
scripts/init_wiki.py	Scaffold a new wiki — creates raw/, wiki/, CLAUDE.md, index.md, log.md, and hot.md. Idempotent.
scripts/append_log.py	Append a ## [YYYY-MM-DD] action | title entry to log.md. Supports flexible log path detection.
scripts/update_index.py	Add or update an entry under a category in index.md. Upserts by (category, title). Flexible index path detection.
scripts/lint_wiki.py	Health check. Detects orphan pages and index drift in both standard markdown and Obsidian wiki-link ([[...]]) format. Default: writes wiki/reports/lint-<today>.md and auto-tracks. Run --stdout for terminal output.
scripts/migrate_wiki.py	Schema upgrade (v1 → v2). Deduplicates index.md, moves dated changelog blocks from hot.md into log.md, stamps the schema version. Idempotent.

Templates

Template	Used for
wiki-CLAUDE.md.tmpl	The schema file dropped into a fresh wiki
source-summary.md.tmpl	One ingested source — claims, methodology, cross-links, open questions
entity-page.md.tmpl	People, organizations, places, products
concept-page.md.tmpl	Ideas, frameworks, theories, terms
comparison-page.md.tmpl	"X vs Y" pages, often filed-back query answers
index.md.tmpl	Initial content catalog
log.md.tmpl	Initial log with bootstrap entry
hot.md.tmpl	Initial hot cache — rewritten after each ingest with latest sources and active references

Reference docs

Eleven detailed workflow documents in references/: philosophy.md · architecture.md · bootstrap-workflow.md · ingest-workflow.md · query-workflow.md · update-workflow.md · lint-workflow.md · migrate-workflow.md · schema-design-guide.md · multi-wiki-routing.md · teaching-mode.md

The skill reads these selectively — you don't need to. They're there to give the LLM depth on each mode.

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Update mode

Standard ingest already handles contradictions on a single page (Disputes section). Update mode is for when a new source supersedes a claim that's paraphrased across multiple pages — the same idea written four different ways in four different files.

Scenario: Smith 2024 reanalysis shows Keys 1980's seven-countries study cherry-picked data.
The Keys r=0.87 claim appears as:
  concepts/saturated-fat.md     → "Keys found r=0.87 across seven countries"
  entities/ancel-keys.md        → "famous for showing strong correlation"
  concepts/heart-disease.md     → "saturated fat is a primary driver per Keys"
  concepts/dietary-policy.md    → "the saturated fat hypothesis drove decades of policy"

Update mode:
  1. Semantic sweep — finds all four (grep won't, LLM will)
  2. Shows scope: "4 pages affected. Proceed?"
  3. Diff-before-write per page — y/n/skip/edit per change
  4. Per-page strategy: revise / disputes / annotate (not one-size-fits-all)
  5. One log entry tying all four edits to Smith 2024

This is change propagation, not change tracking. The log and frontmatter track what was edited. Update mode ensures the edit reaches everywhere it should.

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Auto-dated lint reports

lint_wiki.py with no flags:

• Writes wiki/reports/lint-YYYY-MM-DD.md (overwrites same-day run — idempotent daily)
• Adds a Reports index entry automatically
• Appends a lint | Health check log entry automatically
• Exits with code 1 if any block-severity issue found (useful for CI)

Reports accumulate as a longitudinal health record. git log wiki/reports/ shows how wiki quality evolved over time.

Override flags: --stdout (terminal, no tracking), --no-track (write file, skip index/log), --report PATH (custom path).

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Multi-wiki

Most users start with one wiki. Once you have two — say, a per-project wiki at the working directory plus a long-lived global "second brain" (often an existing Obsidian vault) — the skill routes writes between them based on a single declaration in the project's CLAUDE.md.

~/projects/x-project/          ← active project (current working directory)
├── CLAUDE.md                  ← project schema — declares the global wiki path
├── raw/                       ← project sources
└── wiki/                      ← project wiki

~/Documents/obsidian/          ← global wiki (long-lived, exists across projects)
├── CLAUDE.md                  ← global schema
├── raw/
└── wiki/

One-time setup

Add this to the project's CLAUDE.md (or ask the agent to do it):

## External Wiki

Global knowledge base: ~/Documents/obsidian/

### Routing rules
- Project-specific code decisions, architecture, bugs, configuration → this project's `wiki/`
- Concepts, frameworks, patterns, ideas applicable beyond this project → global wiki
- When in doubt, ask before writing
- Scripts always need `--path` flag pointing to the right wiki root

### Cross-wiki links
- Use absolute paths (`~/...`) when linking from one wiki to the other.
- Never use relative paths that cross wiki boundaries.

Four canonical scenarios

| # | Scenario | Trigger | What the agent does | |