---
name: llm-wiki
description: >
  The foundational knowledge distillation pattern for building and maintaining an AI-powered Obsidian wiki.
  Based on Andrej Karpathy's LLM Wiki architecture. Use this skill whenever the user wants to understand the
  wiki pattern, set up a new knowledge base, or needs guidance on the three-layer architecture (raw sources →
  wiki → schema). Also use when discussing knowledge management strategy, wiki structure decisions, or how
  to organize distilled knowledge. This is the "theory" skill — other skills handle specific operations
  (ingesting, querying, linting).
---

# LLM Wiki — Knowledge Distillation Pattern

You are maintaining a persistent, compounding knowledge base. The wiki is not a chatbot — it is a **compiled artifact** where knowledge is distilled once and kept current, not re-derived on every query.

## Three-Layer Architecture

### Layer 1: Raw Sources (immutable)

The user's original documents — articles, papers, notes, PDFs, conversation logs, bookmarks, **and images** (screenshots, whiteboard photos, diagrams, slide captures). These are never modified by the system. They live wherever the user keeps them (configured via `OBSIDIAN_SOURCES_DIR` in `.env`). Images are first-class sources: the ingest skills read them via the Read tool's vision support and treat their interpreted content as inferred unless it's verbatim transcribed text. Image ingestion requires a vision-capable model — models without vision support should skip image sources and report which files were skipped.

Think of raw sources as the "source code" — authoritative but hard to query directly.

### Layer 2: The Wiki (LLM-maintained)

A collection of interconnected Obsidian-compatible markdown files organized by category. This is the compiled knowledge — synthesized, cross-referenced, and navigable. Each page has:

- YAML frontmatter (title, category, tags, sources, timestamps)
- Obsidian `[[wikilinks]]` connecting related concepts
- Clear provenance — every claim traces back to a source

The wiki lives at the path configured via `OBSIDIAN_VAULT_PATH` in `.env`.

### Layer 3: The Schema (this skill + config)

The rules governing how the wiki is structured — categories, conventions, page templates, and operational workflows. The schema tells the LLM *how* to maintain the wiki.

## Wiki Organization

The vault has two levels of structure: **categories** (what kind of knowledge) and **projects** (where the knowledge came from).

### Categories

Organize pages into these default categories (customizable in `.env`):

| Category | Purpose | Example |
|---|---|---|
| `concepts/` | Ideas, theories, mental models | `concepts/transformer-architecture.md` |
| `entities/` | People, orgs, tools, projects | `entities/andrej-karpathy.md` |
| `skills/` | How-to knowledge, procedures | `skills/fine-tuning-llms.md` |
| `references/` | Summaries of specific sources | `references/attention-is-all-you-need.md` |
| `synthesis/` | Cross-cutting analysis across sources | `synthesis/scaling-laws-debate.md` |
| `journal/` | Timestamped observations, session logs | `journal/2024-03-15.md` |

### Projects

Knowledge often belongs to a specific project. The `projects/` directory mirrors this:

```
$OBSIDIAN_VAULT_PATH/
├── projects/
│   ├── my-project/
│   │   ├── my-project.md      ← project overview (named after project)
│   │   ├── concepts/          ← project-scoped category pages
│   │   ├── skills/
│   │   └── ...
│   ├── another-project/
│   │   └── ...
│   └── side-project/
│       └── ...
├── concepts/                   ← global (cross-project) knowledge
├── entities/
├── skills/
└── ...
```

**When knowledge is project-specific** (a debugging technique that only applies to one codebase, a project-specific architecture decision), put it under `projects/<project-name>/<category>/`.

**When knowledge is general** (a concept like "React Server Components", a person like "Andrej Karpathy", a widely applicable skill), put it in the global category directory.

**Cross-referencing:** Project pages should `[[wikilink]]` to global pages and vice versa. A project's overview page should link to the key concept, skill, and entity pages relevant to that project — whether they live under the project or globally.

**Naming rule:** The project overview file must be named `<project-name>.md`, not `_project.md`. Obsidian's graph view uses the filename as the node label — `_project.md` makes every project appear as `_project` in the graph, making it unreadable. So `projects/my-project/my-project.md`, `projects/another-project/another-project.md`, etc.

Each project directory has an overview page structured like this:

```markdown
---
title: My Project
category: project
tags: [ai, web, backend]
source_path: ~/.claude/projects/-Users-name-Documents-projects-my-project
created: 2026-03-01T00:00:00Z
updated: 2026-04-06T00:00:00Z
---

# My Project

One-paragraph summary of what this project is.

## Key Concepts
- [[concepts/some-api]] — used for core functionality
- [[projects/my-project/concepts/main-architecture]] — project-specific architecture

## Related
- [[entities/some-service]] — deployment platform
```

## Special Files

Every wiki has these files at its root:

### `index.md`
A content-oriented catalog organized by category. Each entry has a one-line summary and tags. Rebuild this after every ingest operation. Format:

```markdown
# Wiki Index

## Concepts
- [[transformer-architecture]] — The dominant architecture for sequence modeling ( #ml #architecture)
- [[attention-mechanism]] — Core building block of transformers ( #ml #fundamentals)

## Entities
- [[andrej-karpathy]] — AI researcher, educator, former Tesla AI director ( #person #ml)
```
**Format rule**: Add a space after the opening `(` and tags.
❌ Don't: `description (#tag)` — breaks tag parsing
✅ Do: `description ( #tag)` — proper spacing and tag parsing

### `log.md`
Chronological append-only record tracking every operation. Each entry is parseable:

```markdown
## Log

- [2024-03-15T10:30:00Z] INGEST source="papers/attention.pdf" pages_updated=12 pages_created=3
- [2024-03-15T11:00:00Z] QUERY query="How do transformers handle long sequences?" result_pages=4
- [2024-03-16T09:00:00Z] LINT issues_found=2 orphans=1 contradictions=1
- [2024-03-17T10:00:00Z] ARCHIVE reason="rebuild" pages=87 destination="_archives/..."
- [2024-03-17T10:05:00Z] REBUILD archived_to="_archives/..." previous_pages=87
```

### `.manifest.json`
Tracks every source file that has been ingested — path, timestamps, what wiki pages it produced. This is the backbone of the delta system. See the `wiki-status` skill for the full schema.

The manifest enables:
- **Delta computation** — what's new or modified since last ingest
- **Append mode** — only process the delta, not everything
- **Audit** — which source produced which wiki page
- **Staleness detection** — source changed but wiki page hasn't been updated

## Page Template

When creating a new wiki page, use this structure:

```markdown
---
title: Page Title
category: concepts
tags: [ml, architecture]
aliases: [alternate name]
relationships:
  - target: "[[concepts/related-concept]]"
    type: extends
sources: [papers/attention.pdf]
summary: One or two sentences, ≤200 chars, so a reader (or another skill) can preview this page without opening it.
provenance:
  extracted: 0.72
  inferred: 0.25
  ambiguous: 0.03
base_confidence: 0.65
lifecycle: draft
lifecycle_changed: 2024-03-15
tier: supporting
created: 2024-03-15T10:30:00Z
updated: 2024-03-15T10:30:00Z
---

# Page Title

One-paragraph summary of what this page covers.

## Key Ideas

- The source's central claim, paraphrased directly.
- A generalization the source implies but doesn't state outright. ^[inferred]
- A figure two sources disagree on. ^[ambiguous]

Use [[wikilinks]] to connect to related pages.

## Open Questions

Things that are unresolved or need more sources.

## Sources

- [[references/attention-is-all-you-need]] — Original paper
```

## Provenance Markers

Every claim on a wiki page has one of three provenance states. Mark them inline so the reader (and future ingest passes) can tell signal from synthesis.

| State | Marker | Meaning |
|---|---|---|
| **Extracted** | *(no marker — default)* | A paraphrase of something a source actually says. |
| **Inferred** | `^[inferred]` suffix | An LLM-synthesized claim — a connection, generalization, or implication the source doesn't state directly. |
| **Ambiguous** | `^[ambiguous]` suffix | Sources disagree, or the source is unclear. |

Example:

```markdown
- Transformers parallelize across positions, unlike RNNs.
- This is why they scale better on modern hardware. ^[inferred]
- GPT-4 was trained on roughly 13T tokens. ^[ambiguous]
```

**Why this syntax:**
- `^[...]` is footnote-adjacent in Obsidian — renders cleanly and never collides with `[[wikilinks]]`.
- Inline (suffix) so a single bullet stays a single bullet.
- Default = extracted means existing pages without markers stay valid.

**Frontmatter summary:** Optionally surface the rough mix at the page level so the user can scan for speculation-heavy pages without reading them:

```yaml
provenance:
  extracted: 0.72   # rough fraction of sentences/bullets with no marker
  inferred: 0.25
  ambiguous: 0.03
```

These are best-effort numbers written by the ingest skill at create/update time. `wiki-lint` recomputes them and flags drift. The block is optional — pages without it are treated as fully extracted by convention.

## Typed Relationships

Plain `[[wikilinks]]` in page bodies carry no semantic weight — they indicate "related to" but not *how*. The optional `relationships:` frontmatter block adds typed, directional edges to the knowledge graph.

### The `relationships:` block

```yaml
relationships:
  - target: "[[Transformer Architecture]]"
    type: extends
  - target: "[[LSTM]]"
    type: contradicts
  - target: "[[Attention Mechanism]]"
    type: implements
```

Each entry has two required fields:
- `target` — a wikilink (using the same format as `OBSIDIAN_LINK_FORMAT`) to the related page
- `type` — one of the allowed semantic types below

### Allowed relationship types

| Type | Meaning | Example |
|---|---|---|
| `extends` | This page builds on or generalises the target | GPT extends Transformer Architecture |
| `implements` | This page is a concrete realisation of the target concept | BERT implements Masked Language Modelling |
| `contradicts` | This page's claims conflict with or refute the target | Evidence A contradicts Evidence B |
| `derived_from` | This page is based on or adapted from the target | Fine-tuning is derived from Transfer Learning |
| `uses` | This page depends on or relies on the target | RAG uses Vector Databases |
| `replaces` | This page supersedes or deprecates the target | GPT-4 replaces GPT-3 |
| `related_to` | Catch-all: related but no stronger directional type applies | Concept A is related to Concept B |

### Rules

- **Optional field** — omit the block entirely if no typed relationships are known. Untagged wikilinks remain valid and are treated as `related_to` by `wiki-export`.
- **Don't duplicate** — if `[[foo]]` already appears as an inline wikilink, the `relationships:` entry just enriches it with a type; it is not a second link.
- **Direction matters** — the page declaring the entry is the *source*; `target` is the destination. Only declare relationships from this page's perspective.
- **Don't fabricate** — only add a typed entry when the source material makes the relationship direction and type clear. When in doubt, use `related_to` or omit.

Skills that read `relationships:`: `wiki-export` (emits typed edges), `cross-linker` (writes typed entries when inferring links), `wiki-query` (may surface type in answers).

## Confidence and Lifecycle

Every page carries two orthogonal trust signals plus an optional supersession link.

### Required fields

```yaml
base_confidence: 0.65          # [0.0, 1.0] — time-independent quality estimate. Stored once, recomputed on content change.
lifecycle: draft               # draft | reviewed | verified | disputed | archived
lifecycle_changed: 2024-03-15  # ISO date of last state transition
# lifecycle_reason: "..."      # optional free-text — why the state changed; surfaced by wiki-query
# superseded_by: "[[new-page]]" # wikilink; only when lifecycle=archived
```

`lifecycle_reason` and `superseded_by` are optional. Never fabricate them.

### Confidence formula

```
base_confidence = source_count_score * 0.5 + source_quality_score * 0.5

source_count_score   = min(distinct_source_ids / 3, 1.0)
source_quality_score = avg(quality score per distinct source_id)
```

**Source-quality scores** (use the highest-matching bucket):

| Bucket | Score | Examples |
|---|---|---|
| `paper` | 1.0 | arXiv, conference proceedings |
| `official` | 0.9 | `*.gov`, vendor docs |
| `documentation` | 0.85 | well-maintained third-party docs |
| `book` | 0.8 | books, technical references |
| `repository` | 0.75 | GitHub READMEs, codebases |
| `blog` | 0.55 | personal blogs |
| `session_transcript` | 0.5 | conversation history |
| `forum` | 0.4 | Stack Overflow, HN, Reddit |
| `unknown` | 0.4 | catch-all |
| `llm_generated` | 0.3 | LLM self-reflections |

**A `source_id`** is a stable per-source identifier — prevents counting three copies of the same blog as three distinct sources:

| Source type | source_id rule |
|---|---|
| Academic paper | DOI > arXiv ID > `<author>-<year>-<slug>` |
| GitHub repo | `github.com/<owner>/<repo>` |
| Documentation site | `<canonical-host>/<product>` |
| Blog post | `<host>/<author>` |
| Session transcript | `<agent>/<session-id>` |
| Other | `<canonical-url>` |

**Per-skill defaults** (ingest skills compute this automatically):

| Skill | base_confidence | lifecycle |
|---|---|---|
| `ingest-url` | `0.17 + 0.5 × classify(url)` | `draft` |
| `wiki-ingest` (single doc) | per-source classifier | `draft` |
| `wiki-ingest` (multi-doc) | `min(N/3,1)×0.5 + avg_q×0.5` | `draft` |
| `wiki-research` | varies, often 0.85+ | `draft` |
| `wiki-capture` | 0.42 | `draft` |
| `*-history-ingest` | 0.42 | `draft` |
| `wiki-update` | 0.59 | `draft` |
| `wiki-synthesize` | `min(input_pages.base_confidence)` | `draft` |
| `data-ingest` | 0.37 | `draft` |

### Lifecycle state machine

Five states. **`stale` is not a state** — it is a computed overlay: `is_stale = (today − updated) > 90 days`.

| State | Entered by | Notes |
|---|---|---|
| `draft` | Any ingest skill on first write | Default for all new pages |
| `reviewed` | Human edit only | |
| `verified` | Human edit only | Time alone never demotes verified pages |
| `disputed` | Manual edit only | Overrides every state except `archived` in display |
| `archived` | Manual edit, or ingest skill setting `superseded_by` | Terminal |

Only ingest skills set `draft`. All other transitions require a human editor. Update `lifecycle_changed` whenever the state changes.

## Importance Tiering

The `tier:` field controls which pages get updated on each ingest pass and their priority in retrieval. As wikis grow, re-reading every page on every ingest wastes tokens — tiering lets ingest and query skills focus effort where it matters most.

### Three tiers

| Tier | Meaning | Ingest behavior | Query priority |
|---|---|---|---|
| `core` | Load-bearing pages — many other pages depend on them (high incoming-link count or bridge position). Always worth updating. | Always update if the source is even marginally relevant | Surfaced first in index and full-read passes |
| `supporting` *(default)* | Standard wiki pages with moderate connectivity | Update when the source has clear new claims for this page | Standard priority |
| `peripheral` | Low-connectivity pages — rarely linked, narrowly scoped | Skip unless the source is *primarily* about this topic | Last resort; skipped when trimming to context budget |

### Assignment rules

- **New pages:** default to `tier: supporting`
- **Promote to `core`:** when a page accumulates ≥5 incoming wikilinks **or** is flagged as a bridge by `wiki-status` insights mode
- **Demote to `peripheral`:** when a page has ≤1 incoming link and hasn't been updated in 90+ days
- **Human override always wins** — edit `tier:` manually to lock a page at any level
- Existing pages without `tier:` are treated as `supporting` (backward compatible — no migration needed)

### Who manages tier

- `wiki-ingest` reads `tier:` to decide whether to update a page on the current pass
- `wiki-query` uses `tier:` to order candidates in the index pass and trim to context budget
- `wiki-status` insights mode computes graph metrics and **suggests** tier assignments — it never writes them automatically
- `wiki-lint` flags missing `tier:` on newly created pages (Phase 2 enforcement, same timeline as `base_confidence`)

## Retrieval Primitives

Reading the vault is the dominant cost of every read-side skill. Use the cheapest primitive that can answer the question and **escalate only when the cheaper one is insufficient**. Any skill that needs content from the vault should follow this table rather than jumping straight to full-page reads.

| Need | Primitive | Relative cost |
|---|---|---|
| Does a page exist? What's its title/category/tags? | Read `index.md`; `Grep` frontmatter blocks (scope with a pattern that targets `^---` blocks at file heads) | **Cheapest** |
| 1–2 sentence preview of a page | Read the `summary:` field in its frontmatter | **Cheap** |
| A specific claim or section inside a page | `Grep -A <n> -B <n> "<term>" <file>` — returns only the matching lines plus context | **Medium** |
| Whole-page content | `Read <file>` | **Expensive** — last resort |
| Relationships across pages | `Grep "\[\[.*?\]\]"` across the vault, or walk wikilinks from a known page | Case-by-case |

**The rule:** escalate only when the cheaper primitive can't answer the question. If you can answer from `summary:` fields alone, don't read page bodies. If a grepped section with `-A 10 -B 2` gives you the claim, don't read the whole page. A 500-line page opened to read 15 lines is 485 lines of wasted tokens.

**Why this matters:** a 20-page vault lets you get away with full-vault scans. A 200-page vault does not. The primitives above are how the skills framework scales to large vaults without a database.

Skills that consume this table: `wiki-query`, `cross-linker`, `wiki-lint`, `wiki-status` (insights mode). Any new skill that reads the vault should cite this section rather than reinvent the pattern.

## QMD Index Freshness

QMD is an optional search index layered on top of the vault. The markdown vault is the source of truth. Any skill that writes wiki markdown should refresh QMD after the vault write completes, but only when `QMD_WIKI_COLLECTION` is configured and the local QMD transport is available. If QMD refresh fails, keep the vault changes and report the QMD status separately.

Use the cheapest verification path that proves the new content is visible: `qmd update`, `qmd embed` only if vectors are stale or missing, then a targeted `qmd get` or `qmd ls` check for one written page or the collection root. Read-only skills should not refresh QMD.

## Core Principles

1. **Compile, don't retrieve.** The wiki is pre-compiled knowledge. When you ingest a source, update every relevant page — don't just create a summary of the source.

2. **Compound over time.** Each ingest should make the wiki smarter, not just bigger. Merge new information into existing pages, resolve contradictions, strengthen cross-references.

3. **Provenance matters.** Every claim should trace to a source. When updating a page, note which source prompted the update.

4. **Mark inferences.** Default sentences are extracted. Mark synthesized claims with `^[inferred]` and contested claims with `^[ambiguous]`. A wiki that hides its guessing rots silently; one that marks it stays trustworthy.

5. **Human curates, LLM maintains.** The human decides what sources to add and what questions to ask. The LLM handles the bookkeeping — updating cross-references, maintaining consistency, noting contradictions.

6. **Obsidian is the IDE.** The user browses and explores the wiki in Obsidian. Everything must be valid Obsidian markdown with working wikilinks.

## Link Format

All internal links connecting wiki pages are controlled by `OBSIDIAN_LINK_FORMAT` from the resolved config (default: `wikilink`).

| Setting | Syntax | Example |
|---|---|---|
| `wikilink` *(default)* | `[[path/to/page]]` or `[[path/to/page\|display text]]` | `[[concepts/foo\|foo]]` |
| `markdown` | `[display text](relative/path.md)` | `[foo](../concepts/foo.md)` |

### Generating markdown-format links

When `OBSIDIAN_LINK_FORMAT=markdown`:
1. Compute the path from the **current file's directory** to the **target `.md` file** using `..` to climb up as needed.
2. Use the page title or a natural phrase as display text.
3. Always include the `.md` extension.

| Current file | Target | Relative link |
|---|---|---|
| `index.md` | `concepts/foo.md` | `[foo](concepts/foo.md)` |
| `concepts/foo.md` | `entities/bar.md` | `[bar](../entities/bar.md)` |
| `projects/my-project/my-project.md` | `concepts/foo.md` | `[foo](../../concepts/foo.md)` |
| `projects/my-project/concepts/arch.md` | `entities/bar.md` | `[bar](../../../entities/bar.md)` |

The `[[path\|display text]]` wikilink form maps to `[display text](relative/path.md)` in Markdown mode.

**Scope:** this setting affects only newly written or updated links. Existing vault content is never automatically migrated — users who want to convert old links can run the `cross-linker` or `wiki-lint` skill.

Every write skill reads `OBSIDIAN_LINK_FORMAT` from config before generating links and applies the correct format.

## Config Resolution Protocol

**All skills must resolve config using this algorithm — do not hard-code `.env` or `~/.obsidian-wiki/config` directly.** This ensures single-vault, multi-vault, project-local, and VPS setups all work correctly.

### Resolution order

1. **Walk up from CWD** — look for a `.env` file in the current directory, then each parent, up to `$HOME`. Stop at the first `.env` that contains `OBSIDIAN_VAULT_PATH`.
2. **Global config** — if no local `.env` found, read `~/.obsidian-wiki/config`.
3. **Prompt setup** — if neither exists, tell the user: "No config found. Run `wiki-setup` to initialize your wiki."

```
find_config() {
  dir="$PWD"
  while [[ "$dir" != "$HOME" && "$dir" != "/" ]]; do
    [[ -f "$dir/.env" ]] && grep -q "OBSIDIAN_VAULT_PATH" "$dir/.env" && { echo "$dir/.env"; return; }
    dir="$(dirname "$dir")"
  done
  [[ -f "$HOME/.obsidian-wiki/config" ]] && { echo "$HOME/.obsidian-wiki/config"; return; }
  echo ""
}
```

### Vault-scoped state

Skills that write runtime state (e.g. `daily-update`) must scope that state to the resolved vault, not to a global path. Use:

```
VAULT_ID=$(echo "$OBSIDIAN_VAULT_PATH" | md5sum 2>/dev/null || md5 -q - <<< "$OBSIDIAN_VAULT_PATH" | cut -c1-8)
STATE_DIR="$HOME/.obsidian-wiki/state/$VAULT_ID"
```

### Standard "Before You Start" block

Every skill's setup section should read:

> **Resolve config** — follow the Config Resolution Protocol in `llm-wiki/SKILL.md`. Walk up from CWD for `.env`, fall back to `~/.obsidian-wiki/config`, else prompt setup. This gives `OBSIDIAN_VAULT_PATH` and any tool-specific path overrides.

## Environment Variables

The wiki is configured through environment variables (see `.env.example`). The only required variable is the vault path — everything else has sensible defaults.

- `OBSIDIAN_VAULT_PATH` — Where the wiki lives **(required)**
- `OBSIDIAN_SOURCES_DIR` — Where raw source documents are
- `OBSIDIAN_CATEGORIES` — Comma-separated list of categories
- `CLAUDE_HISTORY_PATH` — Where to find Claude conversation data
- `CODEX_HISTORY_PATH` — Where to find Codex session data
- `HERMES_HOME` — Where to find Hermes agent data
- `OPENCLAW_HOME` — Where to find OpenClaw data
- `COPILOT_HISTORY_PATH` — Where to find Copilot session data
- `OBSIDIAN_LINK_FORMAT` — Internal link syntax: `wikilink` (default) or `markdown`
- `WIKI_TOKEN_WARN_THRESHOLD` — Emit a warning in `wiki-status` when the full-wiki token estimate exceeds this value (default: `100000`). Set to `0` to disable. See `wiki-status` for the token footprint report.
- `WIKI_STAGED_WRITES` — When `true`, all LLM-written pages go to `_staging/<category>/` for human review before promotion. See `wiki-setup` and `wiki-stage-commit` for details.

No API keys are needed — the agent running these skills already has LLM access built in.

## Modes of Operation

The wiki supports three ingest modes:

| Mode | When to use | What happens |
|---|---|---|
| **Append** | Small delta, incremental updates | Compute delta via manifest, ingest only new/modified sources |
| **Rebuild** | Major drift, fresh start needed | Archive current wiki to `_archives/`, clear, reprocess all sources |
| **Restore** | Need to go back | Bring back a previous archive |

Use `wiki-status` to see the delta and get a recommendation. Use `wiki-rebuild` for archive/rebuild/restore operations.

## Reference

For details on specific operations, see the companion skills:
- **wiki-status** — Audit what's ingested, compute delta, recommend append vs rebuild
- **wiki-rebuild** — Archive current wiki, rebuild from scratch, or restore from archive
- **wiki-ingest** — Distill source documents into wiki pages
- **claude-history-ingest** — Ingest Claude conversation history
- **codex-history-ingest** — Ingest Codex CLI session history
- **data-ingest** — Ingest any raw text data
- **wiki-query** — Answer questions against the wiki
- **wiki-lint** — Audit and maintain wiki health
- **wiki-setup** — Initialize a new vault