Works with Claude Code CLI & GitHub Copilot

Turn research papers into a
living knowledge base

LLM Wiki extracts key concepts from your PDFs, docs, and articles, weaving them into an interconnected, queryable wiki — with zero manual writing.

⭐ Star on GitHub Get started in 3 steps →
llm-wiki — zsh
# Option A — one command (recommended)
/orchestrate-wiki
✔ Empty wiki detected — compiling 5 sources (parallel agents) …
✔ Created wiki/transformer.md · wiki/bert.md · 38 more
✔ Audit passed · Synced README & GitHub Pages

# Option B — step by step
/compile-papers # first run
/sync-wiki # after adding a paper
/audit-wiki # at 20+ pages

# Starting fresh after cloning?
/reset-wiki reset # wipe example pages first

# Query your wiki
/launch-wiki-ui # Streamlit UI at localhost:8501
/stop-wiki-ui # stop when done
# Option A — recommended
> Orchestrate Wiki
✔ Detected empty wiki — compiling sources with parallel agents …
✔ Audit passed · Synced README & GitHub Pages

# Option B — step by step
> Compile Papers to Wiki # first run
> Sync Wiki from Raw # new paper added
> Audit Wiki # at 20+ pages

# Starting fresh after cloning?
> Reset Wiki reset # wipe example pages first

# Query your wiki
> Launch Wiki UI # starts Streamlit at localhost:8501
> Stop Wiki UI # stop when done
>
6+
input formats supported
10
AI-powered skill commands
2
IDEs: Claude Code + Copilot
0
manual wiki pages to write

Everything you need for a serious AI reading practice

Built around the idea that consuming papers is only half the work — structuring what you learn is the other half.

📥

Multi-format ingestion

Accepts PDF, TXT, HTML, DOCX, PPTX, and XLSX. Large PDFs are intelligently chunked so nothing gets dropped.

🔗

Auto-linked entities

Every concept page is rich with [[bracket]] links to related concepts, forming a genuine knowledge graph.

🔄

Incremental sync

Add a new paper and run /sync-wiki. Only changed or new concepts are updated — existing pages are never overwritten needlessly.

🧪

Quality auditing

Run /audit-wiki to surface orphan pages, missing links, contradictions between sources, and stale claims.

💬

Strictly grounded query UI

A Streamlit chat interface queries only your wiki — no hallucinated outside knowledge. Answers cite their source page (e.g. source: bert.md). Unknown topics return an explicit "No information found" with remediation steps.

📖

Source attribution

Every concept traces back to exact papers and pages. Contradictions across sources are captured as features, not hidden.

🛠️

Dual Coding Assistant Tool support

Compile, sync, audit, and reset work in both Claude Code CLI and GitHub Copilot Chat. The interactive query UI is available for both.

🗂️

Git-native

Your wiki lives as plain Markdown files in a git repo. Version control, diffs, and collaboration come for free.

🌐

Web clipping

Pair with the Obsidian Web Clipper browser extension to capture articles and blog posts directly into /raw.

Two approaches, one knowledge base.

Drop sources into /raw — then run the full pipeline in one command, or step through it yourself.

⚡ Recommended
/orchestrate-wiki
💬 Copilot Chat: Orchestrate Wiki
One command runs the full pipeline. It detects your wiki's current state and does the right thing automatically — no flags, no decisions needed.
detects empty wiki → compile detects existing wiki → sync audits with 4 parallel agents syncs README & GitHub Pages
or run each step individually
1

Compile

First run — batch-processes all sources in /raw, extracts concepts, and creates structured entity pages.

/compile-papers
💬 Compile Papers to Wiki
2

Sync

Added a new paper? Sync detects what changed and incrementally updates only the relevant pages.

/sync-wiki
💬 Sync Wiki from Raw
3

Audit

Once you've grown to ~20+ pages, audit checks for orphans, broken links, contradictions, and stale claims.

/audit-wiki
💬 Audit Wiki
⚠ Starting fresh after cloning? The repo ships with example wiki pages. Run /reset-wiki reset before running the pipeline to wipe them and start with your own papers. Without the reset argument, /reset-wiki only reports state — it never deletes anything.
💬 Copilot Chat: Reset Wiki reset

Structured, interlinked, citable

Every generated page follows a consistent template — definition, explanation, related concepts, and sources.

wiki/transformer.md
# Transformer
Neural architecture using self-attention.

## Summary
Introduced in "Attention is All You Need" (2017), the Transformer replaced recurrence with multi-head self-attention, enabling massively parallel training.

## Related Concepts
- [[self-attention]] — core mechanism
- [[positional-encoding]] — injects order
- [[feed-forward-network]] — per-token MLP

## Sources
Vaswani et al. — "Attention is All You Need" (2017)
  • One concept per file, kebab-case filenames keep everything predictable and grep-able.
  • [[bracket]] links create a genuine knowledge graph you can visualise in Obsidian.
  • Sources section traces every claim back to a specific paper and year — no phantom knowledge.
  • Contradictions between sources are documented explicitly, capturing the nuance of the field.
  • Plain Markdown — readable anywhere, no proprietary lock-in.
Topics auto-extracted from papers like:
transformer self-attention BERT scaling laws RLHF foundation models in-context learning emergence hallucination BPE LoRA GPT-3

The same commands, wherever you code

All commands are available flat — no namespaces. Commands work in both Claude Code CLI and GitHub Copilot Chat (Copilot uses slightly different names). The query UI is Claude Code only.

Wiki Skills — build & maintain the knowledge base
orchestrate

/orchestrate-wiki

Claude Code  ·  Copilot: Orchestrate Wiki

One command to run the full pipeline — detects wiki state, compiles or syncs sources using parallel agents, audits quality with parallel agents, then syncs all doc surfaces.

compile

/compile-papers

Claude Code  ·  Copilot: Compile Papers to Wiki

Batch-processes every file in /raw, creates entity pages, and builds the index from scratch. Blocks if wiki already has content — run /reset-wiki first.

sync

/sync-wiki

Claude Code  ·  Copilot: Sync Wiki from Raw

Detects files in /raw not yet logged in wiki/log.md and incrementally updates only the affected pages — existing content is never needlessly overwritten.

audit

/audit-wiki

Claude Code  ·  Copilot: Audit Wiki

Scans for quality issues: orphan pages, missing linked concepts, cross-source contradictions, and stale claims. Run every ~20–30 new pages or before sharing.

reset

/reset-wiki

Claude Code  ·  Copilot: Reset Wiki

Smart state guard: if wiki is empty it scaffolds the index & log; if content exists it summarises and offers options. Pass the reset argument to force-wipe all entity pages.

ui

/launch-wiki-ui

Claude Code  ·  Copilot: Launch Wiki UI

Checks that streamlit and litellm are installed, reports available wiki pages, then starts the Streamlit query interface at localhost:8501.

ui

/stop-wiki-ui

Claude Code  ·  Copilot: Stop Wiki UI

Checks whether the Streamlit process is running, kills it if active, and confirms it is stopped. Companion to /launch-wiki-ui.

Repo Maintenance Skills — keep the repo healthy
docs

/sync-docs

Claude Code  ·  Copilot: Sync Docs

Detects changed files via git diff, maps them to affected doc surfaces (README, GitHub Pages, copilot-instructions), and applies targeted edits — never rewrites entire files.

health

/run-maintenance

Claude Code  ·  Copilot: Run Maintenance

Runs the full pytest suite, verifies every skill is registered in both Claude Code and Copilot, checks wiki health and unsynced sources, inspects git status, and saves a dated report to reports/.

slides

/regenerate-presentation

Claude Code  ·  Copilot: Regenerate Presentation

Detects which generator scripts or skill files changed via git, rebuilds only stale assets (terminal/UI demo videos + PPTX deck), and verifies both videos are embedded in the deck.

Chat with your entire wiki

Run /launch-wiki-ui to open a guided 3-screen Streamlit interface. Configure your model and API key, confirm which wiki pages are loaded, then chat — answers are grounded strictly in your wiki.

Settings Model ID + API key
Wiki Confirmation Review loaded pages
Chat wiki-grounded answers
🤖 LLM Wiki Query — gpt-4o  ·  12 pages loaded ● connected
U
How does BERT's masked language modeling differ from GPT-3's autoregressive approach, and which is better for embeddings?
C
BERT uses a masked language model (MLM) objective — randomly masking 15% of tokens and predicting them bidirectionally. Full left+right context makes BERT representations excellent for classification, NER, and QA tasks where the full sentence is available at inference time.

GPT-3 uses an autoregressive objective — predicting the next token given only left context. This makes it exceptional for generation and few-shot prompting. Your scaling-laws.md page notes that sufficiently large autoregressive models begin to match BERT-style encoders on many benchmarks.

For embeddings specifically, BERT wins — bidirectionality captures richer semantic context per token.
(source: bert.md, gpt3.md, scaling-laws.md)
↑ input 1,204
↓ output 187
⚡ cache read 18,432
✍ cache write 0
U
What is LoRA fine-tuning?
C
No information found in the wiki for this query.
The wiki does not currently cover this topic. To enable answers: add a relevant PDF/DOCX/TXT to raw/, then run /sync-wiki.
Works with any major LLM provider — enter the model ID directly:
gpt-4o claude-opus-4-7 gemini/gemini-2.0-flash mistral/mistral-large-latest cohere/command-r-plus
Security:
API key session-only never written to disk model ID validated

Up and running in minutes

1

Clone & configure

Clone the repo. For the query UI, have an API key ready from any major LLM provider (Anthropic, OpenAI, Google, Mistral, Cohere, etc.). No other setup required.

git clone https://github.com/dev-enthusiast-84/llm-wiki.git

Starting fresh? The repo includes example wiki pages. Run /reset-wiki reset to wipe them before running the pipeline with your own papers.

2

Drop your sources into /raw

PDF, DOCX, TXT, HTML, PPTX, or XLSX — anything goes. The Attention paper, BERT, GPT-3, and Scaling Laws papers are included as examples.

3

Build the wiki

Recommended: run /orchestrate-wiki — detects state, compiles or syncs, audits, and syncs docs in one go.

💬 Copilot Chat: Orchestrate Wiki

Or step by step: /compile-papers first run → /sync-wiki after each new paper → /audit-wiki at 20+ pages.

💬 Copilot Chat: Compile Papers to WikiSync Wiki from RawAudit Wiki
4

Query with /launch-wiki-ui

A 3-screen flow: enter your model ID and API key → confirm loaded wiki pages → chat. Answers are grounded strictly in your wiki and cite the source page. Topics not yet covered return an explicit "No information found" with instructions on which file to add.

💬 Copilot Chat: Launch Wiki UI  ·  Stop Wiki UI

See it in action — demo deck →

Stop re-reading the same papers.
Build the wiki once.

LLM Wiki is open source, MIT licensed, and ready to use today.

⭐ Star on GitHub Fork & customize →