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:

---
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:

# 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:

## 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:

---
title: Page Title
category: concepts
tags: [ml, architecture]
aliases: [alternate name]
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
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:

- 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:

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.

Confidence and Lifecycle

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

Required fields

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.

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.

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 (read from ~/.obsidian-wiki/config or .env, 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

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