llm-wiki

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#javascript #python #react #go #android #rust #docker #nodejs #java #awesome #vue #pytorch #ios #open-source

(★ 1,055)

LLM-compiled knowledge bases for any AI agent. Parallel multi-agent research, thesis-driven investigation, source ingestion, wiki compilation, querying, and artifact generation.

파일 탐색기

최종 버전 다운로드 (.zip)

- - marketplace.json
- release-checklist.md
- marketplace.json
- - ds4-wiki-query.jsonl
  - wiki-query.jsonl
- - pi-payload-metrics.ts
- README.md
- - plugin.json
- - llm-wiki
- - adapter.md
  - archive.md
  - assess.md
  - audit.md
  - checkpoint.md
  - collect.md
  - compile.md
  - dataset.md
  - feedback.md
  - idea.md
  - ingest-collection.md
  - ingest.md
  - inventory.md
  - librarian.md
  - lint.md
  - ll.md
  - output.md
  - plan.md
  - portfolio.md
  - project.md
  - query.md
  - refresh.md
  - research.md
  - retract.md
  - session.md
  - specialist.md
  - thesis.md
  - wiki.md
- - README.md
- - pi-query-tools.ts
  - README.md
- - SKILL.md
- benchmark-token-efficiency
- bootstrap-codex-plugin.sh
- llm-wiki
- llm-wiki-session
- pi-ds4-wiki-query
- pi-wiki-query
- sync-codex-plugin.sh
- sync-opencode-plugin.sh
- sync-query-lite-profile.sh
- verify-codex-plugin.sh
- - token-budgets.json
- - plugin-tests.yml
- - fake-claude-cli.py
  - fake-codex-app-server.py
  - fake-pi-cli.py
- generate-defect-fixtures.sh
- promptfooconfig.yaml
- README.md
- test-codex-runtime.sh
- test-codex-sync.sh
- test-docs-consistency.sh
- test-local-cli-adapters.sh
- test-local-cli-checkpoint.sh
- test-local-cli-lint.sh
- test-local-cli-retract.sh
- test-local-cli-specialists.sh
- test-opencode-sync.sh
- test-plugin-validate.sh
- test-query-lite-sync.sh
- test-session-capture.sh
- test-session-concurrency.sh
- test-structure.sh
- test-token-benchmarks.sh
.gitignore
AGENTS.md
CLAUDE.md
LICENSE
README.md

// repository documentation

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```

[llm-wiki.net](https://llm-wiki.net/) · [@LLMWIKI on X](https://x.com/LLMWIKI) · [github.com/nvk/llm-wiki](https://github.com/nvk/llm-wiki)

LLM-compiled knowledge bases for any AI agent. Capture rough Ideas, research and shape them, then explicitly promote approved briefs into delivery Projects. Also includes parallel research, collector catalogs, session memory, source ingestion, compilation, audits, querying, and artifact generation. Ships for Claude Code, OpenAI Codex, OpenCode, and portable agents. Obsidian-compatible.

---

[Install](#install) · [Quick Start](#quick-start) · [Sessions](#session-memory) · [Commands](#commands) · [How It Works](#how-it-works) · [Research Modes](#research-modes) · [Thesis Research](#thesis-driven-research) · [Query Depths](#query-depths) · [Linking](#linking-works-everywhere) · [Obsidian](#obsidian-integration) · [Architecture](#claude-first-multi-runtime) · [Nono Sandbox](#nono-sandbox-permissions) · [Upgrade](#upgrade) · [Changelog](#changelog) · [Credits](#credits)

---

## Changelog

**v0.24.0** — **Project Knowledge Checkpoints Export.** Exports comprehensive,
cross-topic project handoffs under `docs/knowledge/<slug>/` with
dry-run-first create and refresh, read-only verification and bounded import,
exact source and section coverage, explicit omissions, semantic privacy
minimization, deterministic sealing, attested overrides, and a thin-output
guard. Checkpoint writes never authorize commit, publication, or import.

**v0.23.0** — **Personal specialist framework.** Adds optional user-owned,
instruction-only `SKILL.md` review methods under the user's local wiki hub,
explicit per-topic allowlists, deterministic validation and management, and research
selection with version/hash provenance. The public release contains the
framework only; personal specialist packages and wiki-derived candidate reports
are not bundled or published.

**v0.22.0** — **Declarative private-adapter routing.** Registered adapters
may declare provider-neutral intent and exact-URL routes plus an adapter-owned
workflow guide. The public plugin discovers the route before ingestion but no
longer embeds any provider's authentication, browser, recovery, or editing
workflow.

**v0.21.3** — **Adapter-boundary transition.** Consolidates the v0.21 line and
keeps the session-hook compatibility fix. Provider-specific workflow material
from that line is superseded in current source by manifest-driven routing and
lives only in the corresponding private adapter.

**v0.20.0** — **Governed remote writes.** Extends private adapters with exact
remote-resource allowlists, declared read/write effects, explicit approval
bound to an exact plan hash, expected revisions, stable idempotency keys,
private verified receipts, and content-free terminal reporting.

**v0.19.0** — **Private adapter protocol.** Adds an explicitly trusted,
machine-local adapter registry and portable `llm-wiki-adapter/v1` JSON contract,
with manifest handshakes, path scopes, sanitized environments, hash-verified
artifacts, bundled management CLI, and an explicit workflow boundary that never
passes a wiki destination or auto-promotes adapter output.

**v0.18.0** — **Hub-wide portfolio.** Adds `/wiki:portfolio`, a live read-only view across active topic wikis that lists canonical Ideas and active Projects separately, distinguishes explicitly promoted Projects from direct ones, preserves Concepts as supporting knowledge, and avoids catch-all topics, duplicated records, inferred lineage, and stale portfolio caches.

## Install

**Claude Code** (native plugin):
```bash
claude plugin install wiki@llm-wiki
```

**OpenAI Codex** (marketplace plugin):

Install from GitHub:
```bash
codex plugin marketplace add nvk/llm-wiki
codex plugin add wiki@llm-wiki
# Start a new Codex thread, then use @wiki or type $ to select wiki-query
```

Install from a local checkout with the managed bootstrap helper:
```bash
./scripts/bootstrap-codex-plugin.sh --scope user --verify
```

Or register the local checkout manually:
```bash
codex plugin marketplace add /absolute/path/to/llm-wiki
codex plugin add wiki@llm-wiki
```

Canonical explicit invocation:
```text
$wiki-query "What does the wiki say about hardware wallet threat models?"
@wiki research "hardware wallet threat models"
@wiki collect "bitcoin memes" --wiki memes-bitcoin
@wiki ingest https://example.com/article
@wiki audit --project coldcard-threat-model
@wiki session status
@wiki feedback list --unpromoted
@wiki session disable   # optional opt-out
@wiki ll "codex plugin install gotchas"
```

Upgrade:
```bash
codex plugin marketplace upgrade llm-wiki
codex plugin add wiki@llm-wiki
```

Remove:
```bash
codex plugin remove wiki@llm-wiki
codex plugin marketplace remove llm-wiki
```

Troubleshooting:
- `codex plugin marketplace add` registers the catalog; `codex plugin add wiki@llm-wiki` installs and enables the cached plugin non-interactively.
- Open `/hooks` to review and trust the bundled hooks if you want automated session capture. The `@wiki` skill works without hook trust.
- `$wiki-query` is the small, explicit, read-only skill for lookups. In Codex CLI/IDE, type `$` or open `/skills` and select it. It never activates implicitly or changes wiki files.
- `@wiki` is the full research and maintenance entry point. Natural-language wiki requests can still auto-activate it.
- Restart Codex after changing config if an existing session does not pick up the new plugin state.
- If you run Codex under a sandbox wrapper like `nono`, see [Nono Sandbox Permissions](#nono-sandbox-permissions) — Codex needs r+w to `$HOME/.codex` for plugin install.

**OpenCode** (instruction file):

Add to your `opencode.json` (project-level or `~/.config/opencode/.opencode.json` for global):
```json
{
  "instructions": ["https://raw.githubusercontent.com/nvk/llm-wiki/master/plugins/llm-wiki-opencode/skills/wiki-manager/SKILL.md"],
  "permission": {
    "external_directory": {
      "~/.config/llm-wiki/**": "allow",
      "~/Library/Mobile Documents/com~apple~CloudDocs/wiki/**": "allow"
    }
  }
}
```

OpenCode fetches the URL fresh on every session start — no manual updates needed. If you prefer a local copy instead:
```bash
curl -sL https://raw.githubusercontent.com/nvk/llm-wiki/master/plugins/llm-wiki-opencode/skills/wiki-manager/SKILL.md > ~/.config/opencode/AGENTS.md
```

For a smaller read-only setup, use the best-effort query preset instead:

```json
{
  "instructions": ["https://raw.githubusercontent.com/nvk/llm-wiki/master/plugins/llm-wiki-opencode/skills/wiki-query/SKILL.md"]
}
```

The OpenCode profile is sync- and budget-tested, but not tied to one model, so
it does not have a provider-specific live quality gate. Treat it as a portable
best-effort preset and keep OpenCode's write and shell permissions disabled for
query-only sessions.

The `external_directory` permission is required because the wiki hub lives outside the project directory. Set the paths to match your hub location. Alternatively, use `--local` mode (`.wiki/` in the project) to skip permissions entirely.

Web search requires `export OPENCODE_ENABLE_EXA=1`.

**Pi** (skill file, best for local models):

Pi's minimal system prompt leaves room for on-demand wiki workflows on local
models. Load the full skill for research and write-capable maintenance:

```bash
pi --skill path/to/llm-wiki/plugins/llm-wiki-opencode/skills/wiki-manager/SKILL.md
```

Invoke it as `/skill:wiki-manager`, or let Pi load it when the request clearly
matches its description.

For fast read-only queries with Pi's currently configured provider, use the
generic launcher. It disables discovery and write tools and loads the compact
shared query protocol:

```bash
./scripts/pi-wiki-query
```

For DS4, the provider-specific launcher additionally creates an isolated Pi
state directory and pins the local model settings:

```bash
./scripts/pi-ds4-wiki-query
```

Set `PI_CLI`, `DS4_BASE_URL`, or `LLM_WIKI_PI_DS4_STATE_DIR` only when your
local setup differs from the defaults. Both launchers accept `--dry-run` to
show the exact command. The equivalent generic Pi settings are:

```bash
pi \
  --append-system-prompt path/to/llm-wiki/profiles/query-lite/SKILL.md \
  --tools read,grep,find,ls \
  --no-extensions --no-skills --no-prompt-templates --no-themes
```

The DS4 query profile is intentionally unable to write. Switch to the full
skill for ingest, research, compile, lint, or other mutating workflows. See
[`profiles/ds4/README.md`](profiles/ds4/README.md) and the reproducible
[`benchmarks/README.md`](benchmarks/README.md) DS4 lane.

**Any LLM Agent** (portable instruction file):
```bash
# Read-only queries: small default
cp profiles/query-lite/SKILL.md ~/your-project/AGENTS.md

# Research and maintenance: complete protocol
cp AGENTS.md ~/your-project/AGENTS.md
```

The query-lite profile works with agents that can read and search files. The
root `AGENTS.md` contains the complete write-capable protocol for agents that
can also edit files and search the web.

## Claude-First, Multi-Runtime

Claude Code is the principal user. Keep one shared behavior layer and thin packaging layers per runtime:

- `claude-plugin/` is the primary distribution target and UX surface.
- `claude-plugin/skills/wiki-manager/` is the behavioral source of truth.
- `plugins/llm-wiki/skills/wiki/` is the generated Codex packaging target behind `@wiki`.
- `claude-plugin/skills/wiki-manager/references/query-lite.md` is the canonical read-only query protocol.
- `profiles/query-lite/SKILL.md` and generated `wiki-query` skills expose that protocol without the full research context.
- `plugins/llm-wiki-opencode/` is the OpenCode and Pi packaging target.
- `.agents/plugins/marketplace.json` makes the Codex plugin installable from this repo.
- `AGENTS.md` is the portable single-file protocol for any other LLM agent.

**Query and research presets:**

| Client | Read-only query path | Full research path | Validation |
|--------|----------------------|--------------------|------------|
| Claude Code | `/wiki:query` command plus shared query protocol | Native plugin skill and commands | Deterministic fixtures plus live Sonnet/Opus runs |
| Codex | Explicit-only `$wiki-query` (~2.8 KB) | `@wiki` (~11.7 KB before lazy references) | Deterministic fixtures plus app-server live runs |
| Pi / DS4 | `scripts/pi-wiki-query`, or the isolated DS4 launcher, with read-only tools (~2.8 KB profile) | `pi --skill .../wiki-manager/SKILL.md` | Deterministic fixtures plus exact DS4 provider-payload measurement |
| OpenCode | `wiki-query/SKILL.md` (~2.8 KB) | `wiki-manager/SKILL.md` (~25.2 KB) | Static budgets and generated-package sync; live model is best effort |
| Any agent | Copy `profiles/query-lite/SKILL.md` (~2.8 KB) | Copy root `AGENTS.md` (~51.2 KB) | Static budgets |

Sizes are checked-in UTF-8 bytes, not provider token estimates. Use query mode
for lookups, evidence checks, lists, and inventory status. Use the full profile
for research, ingestion, compilation, lint fixes, or any workflow that writes.

Both runtime mirrors are generated, not hand-maintained. Rebuild from the Claude source of truth:

```bash
./scripts/sync-codex-plugin.sh      # regenerates plugins/llm-wiki/
./scripts/sync-opencode-plugin.sh   # regenerates plugins/llm-wiki-opencode/
./scripts/sync-query-lite-profile.sh # regenerates profiles/query-lite/
```

Each sync script:

- copies `claude-plugin/skills/wiki-manager/SKILL.md` into the target tree and reapplies a small list of runtime-specific wording patches
- copies `references/` from the Claude source — references are runtime-neutral and shared verbatim (previously a symlink, now a real copy so Codex marketplace caching works)
- generates compact `wiki-query` packages from the canonical query-lite reference
- (Codex only) recreates `agents/openai.yaml` for Codex UI metadata and syncs the plugin version

Drift is caught by `./tests/test-codex-sync.sh` and `./tests/test-opencode-sync.sh`, which run the sync scripts and fail (with self-healing fix instructions) if the generated directories differ from `HEAD`.

Practical rule: design workflows first for Claude commands and behavior, but keep the underlying knowledge model and references runtime-neutral. Runtime wrappers adapt invocation and metadata, not wiki logic.

## Nono Sandbox Permissions

If you run any AI coding agent inside a [nono](https://github.com/always-further/nono) sandbox, the wiki needs filesystem access beyond the default profile.

### Claude Code / OpenCode

```json
{
  "extends": "claude-code",
  "policy": {
    "add_allow_read": [
      "$HOME/.config/llm-wiki"
    ],
    "add_allow_readwrite": [
      "$HOME/Library/Mobile Documents/com~apple~CloudDocs/wiki"
    ]
  }
}
```

Replace `"extends": "claude-code"` with `"opencode"` for OpenCode.

### Codex

Codex needs r+w to its own `$HOME/.codex` directory for plugin install, marketplace cache, state, and skill registration:

```json
{
  "extends": "codex",
  "policy": {
    "add_allow_read": [
      "$HOME/.config/llm-wiki"
    ],
    "add_allow_readwrite": [
      "$HOME/.codex",
      "$HOME/Library/Mobile Documents/com~apple~CloudDocs/wiki"
    ]
  }
}
```

### Path reference

| Path | Access | Purpose |
|------|--------|---------|
| `$HOME/.config/llm-wiki` | read | Hub path config — checked first during resolution (v0.4.2+) |
| Wiki data dir | readwrite | The wiki itself — use the actual path, not `$HOME/wiki` (see below) |
| `$HOME/.codex` | readwrite | Codex only — plugin cache, skills, state, marketplace temp files |

### Hub resolution and `~/wiki`

Hub resolution checks `~/.config/llm-wiki/config.json` first and only falls back to `~/wiki` when no config exists. If your wiki lives on iCloud or any non-default path, set the config and you don't need `$HOME/wiki` in the sandbox at all:

```bash
# Set once — agents will resolve from config, never touch ~/wiki
/wiki config hub-path "~/Library/Mobile Documents/com~apple~CloudDocs/wiki"
```

Use a portable `hub_path` with `~` for iCloud-shared hubs. Older configs may
contain `resolved_path`; llm-wiki treats it as a fallback cache because an
absolute `/Users/<name>/...` path from one Mac will not be valid on another.
The shared `wikis.json` should likewise store hub topic paths as
`topics/<slug>`, not absolute user-home paths.

If you prefer `~/wiki` as a symlink to iCloud, nono's Seatbelt follows symlinks — the target path must be allowed, not the symlink itself.

### Diagnosing access issues

Without the right permissions, Seatbelt or macOS privacy controls can block file
access. A useful diagnostic pattern is: `stat` succeeds for the iCloud wiki path,
but reading `wikis.json` or listing `topics/` fails with `Operation not
permitted`. That means the configured `hub_path` is correct; grant Full Disk
Access or iCloud Drive access to the exact app launching the agent, restart it,
and do not switch to a machine-local `resolved_path` or `~/wiki` fallback. Use
`nono why` to diagnose sandbox rules:

```bash
nono why --path ~/.config/llm-wiki --op read
nono why --path ~/Library/Mobile\ Documents/com~apple~CloudDocs/wiki --op readwrite
```

**OpenCode** also needs the `external_directory` permission in `opencode.json` (see [Install](#install)) — nono and OpenCode have independent sandboxes that both need the same paths allowed.

## Upgrade

Agents and sandboxed sessions should use GitHub CLI web login with HTTPS git
transport, not SSH. This avoids SSH host-key prompts and `known_hosts` writes
inside nono:

```bash
gh auth login --web --git-protocol https
gh auth setup-git
```

**Claude Code** — if `claude plugin update` pulls the latest correctly:
```bash
git -C ~/.claude/plugins/marketplaces/llm-wiki remote set-url origin https://github.com/nvk/llm-wiki.git
claude plugin update wiki@llm-wiki
# Restart Claude Code to apply
```

If the update command doesn't pick up the new version (stale marketplace cache), sync manually from the repo:
```bash
# Clone or pull the latest
git clone https://github.com/nvk/llm-wiki.git  # or: git -C ~/llm-wiki pull

# Sync plugin files to Claude Code's plugin cache
REPO=~/llm-wiki/claude-plugin
DEST=~/.claude/plugins/cache/llm-wiki/wiki
VERSION=$(grep '"version"' "$REPO/.claude-plugin/plugin.json" | grep -o '[0-9.]*')
rm -rf "$DEST"/*
mkdir -p "$DEST/$VERSION"
cp -R "$REPO/.claude-plugin" "$REPO/commands" "$REPO/skills" "$DEST/$VERSION/"

# Restart Claude Code to apply
```

**Codex** — upgrade from the marketplace:
```bash
codex plugin marketplace upgrade llm-wiki
codex plugin add wiki@llm-wiki
```

**OpenCode** — if using the GitHub URL in `instructions`, updates are automatic (fetched every session). If using a local copy:
```bash
curl -sL https://raw.githubusercontent.com/nvk/llm-wiki/master/plugins/llm-wiki-opencode/skills/wiki-manager/SKILL.md > ~/.config/opencode/AGENTS.md
```

**AGENTS.md** — just pull the latest and replace:
```bash
curl -sL https://raw.githubusercontent.com/nvk/llm-wiki/master/AGENTS.md > ~/your-project/AGENTS.md
```

Check your installed version:
- Claude Code: look for the version in `/wiki` status output or check `~/.claude/plugins/installed_plugins.json`
- Codex: run `./scripts/verify-codex-plugin.sh --scope user` and confirm the installed cache path and marketplace source match this repo

> **New to a topic? One command, from anywhere:**
> ```
> /wiki:research "gut microbiome" --new-topic --min-time 1h
> ```
> Creates a topic wiki, launches parallel agents, and keeps researching for an hour — drilling into subtopics each round finds. Come back to a fully compiled wiki.

## Quick Start

```
/wiki:research "nutrition" --new-topic            # Create wiki + research in one shot
/wiki:research "gut-brain axis" --wiki nutrition   # Add more research to existing wiki
/wiki:research "fasting" --deep --min-time 2h     # 8 agents, keep going for 2 hours
/wiki:research "keto" --retardmax                 # 10 agents, max speed, ingest everything
/wiki:specialist suggest --wiki all                # Rank reusable personal expert methods from current topic indexes
/wiki:research "causal evidence" --specialist research-methodologist  # Apply one enabled bounded review method
/wiki:research "What makes long form articles go viral?" --new-topic  # Question → decompose → playbook
/wiki:thesis "fiber reduces neuroinflammation via SCFAs"  # Thesis-driven: evidence for + against → verdict
/wiki:thesis "cold exposure upregulates BDNF" --min-time 1h  # Deep thesis investigation
/wiki:collect "bitcoin memes" --wiki memes-bitcoin  # Find, dedupe, download media, catalog, and optionally inventory artifacts
/wiki:collect "bitcoin memes" --scale medium --media reference --inventory corpus  # Catalog media without binary downloads
/wiki:query "How does fiber affect mood?"         # Ask the wiki
/wiki:query "compare keto and mediterranean" --deep  # Deep cross-referenced answer
/wiki:query --resume                              # Where did I leave off?
/wiki add https://example.com/article             # Fuzzy router detects URL → ingest
/wiki what do we know about CRISPR?               # Fuzzy router detects question → query
/wiki:ingest https://example.com/article          # Manually ingest a source
/wiki:ingest --inbox                              # Process files dropped in inbox/
/wiki:ingest-collection https://github.com/bitcoin/bips --wiki bitcoin  # Bulk import spec repos
/wiki:ingest-collection https://dump.bitcoin.it/dump_20260429_en.xml.bz2 --wiki bitcoin  # Import MediaWiki dumps
/wiki:ingest-collection messages.csv --adapter csv-messages --wiki bitcoin  # Split message archives
/wiki:ingest-collection "https://example.com/*" --adapter wayback-cdx --from 20100101 --to 20200101  # Import archived snapshots
/wiki:inventory add ingest-candidate "Bitcointalk archive" --wiki bitcoin  # Track source queues and next actions
/wiki:inventory add item "TRX-4M ring and pinion" --wiki trx4m-1-18  # Track actual parts, tools, hosts, or assets
/wiki:inventory list --view actions --limit 10   # Compact chat table of current inventory next actions
/wiki:inventory scan-outputs --dry-run          # Preview queues/backlogs before any inventory pivot
/wiki:dataset add "Bitcointalk Temporal Graph" --location https://figshare.com/articles/dataset/BitcoinTemporalGraph/26305093 --wiki bitcoin  # Index data that stays external
/wiki:dataset list --view schema --limit 10      # Compact chat table of dataset schema/readiness state
/wiki:dataset scan-outputs --dry-run            # Find legacy data reports that could become dataset manifests
/wiki:archive topic old-interest --reason "No longer active"  # Preserve a topic but hide it from normal context
/wiki:archive list --archived                   # Show active and archived topic wikis
/wiki:archive restore old-interest              # Bring an archived topic back
/wiki:compile                                     # Compile any unprocessed sources
/wiki:audit --project gut-brain-playbook          # Truth-seeking audit across outputs + wiki + fresh research
/wiki:output report --topic gut-brain             # Generate a report
/wiki:output slides --retardmax                   # Ship a rough slide deck NOW
/wiki:checkpoint create my-project --repo . --audience team  # Preview a comprehensive cross-topic, privacy-sealed project handoff
/wiki:checkpoint create my-project --repo . --audience team --apply  # Stage, seal, verify, then write; never commit/push
/wiki:checkpoint verify docs/knowledge/my-project # Recheck hashes and the privacy attestation
/wiki:assess /path/to/my-app --wiki nutrition     # Gap analysis: repo vs wiki vs market
/wiki:lint --fix                                  # Clean up inconsistencies
```

When working from this repository checkout, you can also run deterministic
checks without an agent:

```bash
./scripts/llm-wiki lint /path/to/wiki
./scripts/llm-wiki lint --fix /path/to/wiki
./scripts/llm-wiki schema status /path/to/wiki
./scripts/llm-wiki schema adopt /path/to/wiki          # add starter topic guide
./scripts/llm-wiki schema adopt --dry-run /path/to/wiki # preview without writing
./scripts/llm-wiki archive --hub /path/to/hub topic old-interest --reason "No longer active"
./scripts/llm-wiki archive --hub /path/to/hub list --archived
./scripts/llm-wiki archive --hub /path/to/hub restore old-interest
./scripts/llm-wiki-session --hub /path/to/hub status
./scripts/llm-wiki-session --hub /path/to/hub disable   # optional opt-out
./scripts/llm-wiki-session --hub /path/to/hub enable --mode balanced --tool-events 50
./scripts/llm-wiki-session --hub /path/to/hub rehydrate --cwd "$PWD"
./scripts/llm-wiki-session --hub /path/to/hub feedback list --unpromoted
./scripts/llm-wiki adapter add /private/adapter --read-root /private/input --write-root /private/results
./scripts/llm-wiki adapter doctor <id>
./scripts/llm-wiki adapter run <id> --request /absolute/request.json --json
./scripts/llm-wiki adapter run <id> --request /absolute/apply.json \
  --response /private/results/receipt.json \
  --approve-remote-write <plan-sha256> --json
./scripts/llm-wiki specialist init
./scripts/llm-wiki specialist create research-methodologist \
  --description "Reviews study design, causal claims, evidence quality, and reproducibility."
./scripts/llm-wiki specialist validate
./scripts/llm-wiki specialist enable research-methodologist --wiki nutrition
./scripts/llm-wiki specialist list --wiki nutrition --json
./scripts/llm-wiki checkpoint seal docs/knowledge/my-project --audience team --json
./scripts/llm-wiki checkpoint verify docs/knowledge/my-project --json
```

This local helper covers structural checks and safe migrations that do not
require an LLM. Checkpoint sealing is mandatory for generated project
handoffs: it enforces comprehensive input-to-section coverage and a
deterministic thin-output floor, hashes the bundle, scans for sensitive
information without printing matched values, and writes `privacy-report.json`.
There is no no-scan option; intentional exceptions name exact finding IDs and
remain visibly attested as `overridden`. The agentic `/wiki:lint` workflow remains the full protocol for
editorial and deep verification passes. The local schema helper creates only a
starter advisory topic guide (`schema.md`); run librarian conventions advice
for established wikis before adopting topic-specific vocabulary. The local archive helper
performs the deterministic folder move plus `wikis.json`, hub index, and log
updates.

## Personal Specialist Skills

An optional user-owned library under `HUB/.skills/` stores reusable
Agent Skills-compatible `SKILL.md` methods. Specialists encode bounded evidence
and review protocols—not simulated CFO, physician, MBA, or PhD credentials.
They are explicitly enabled per active topic, instruction-only in v1, and
cannot grant tools, writes, subagents, or professional authority.

Research can select zero to three enabled specialists (normally one), give each
the same bounded evidence packet, and record its version and content hash in
provenance. `/wiki:specialist suggest` examines current topic indexes and ranks
candidate methods without creating them; `/wiki:specialist apply` performs a
bounded review. See the [specialist reference](claude-plugin/skills/wiki-manager/references/specialists.md)
for local storage, sharing boundaries, validation, selection, high-stakes
escalation, and eval rules.

## Session Memory

Long agent runs can lose useful context when a chat compacts, a terminal closes,
or work moves between runtimes. LLM Wiki keeps a separate operational-memory
layer under `HUB/.sessions/` (or `.wiki/.sessions/` for a local wiki) so a later
turn can recover the thread without copying full transcripts into the knowledge
base.

| Feature | How it works |
|---------|--------------|
| **Capture** | Trusted hooks use balanced mode by default. They record harness metadata, current directory and Git context, small redacted events, per-session state, and Markdown digests. Full transcript bodies are not stored by default. |
| **Session ID** | An ID such as `codex:abc123` combines the harness name with that runtime's native session ID. It is a local lookup key—not a secret, transcript, wiki, or topic ID. |
| **Rehydrate** | `/wiki:session rehydrate` returns a compact context block and pointers to matching digests instead of bulk-pasting chat history. |
| **Feedback** | High-signal corrections, preferences, approvals, and plan acceptance become reviewable candidates under `.sessions/feedback/`; generic acknowledgements are ignored. |
| **Promote** | Digests and feedback remain operational memory until an explicit `promote` writes a distilled note to a topic's `raw/notes/`. Only then can normal compilation turn it into topic knowledge. |
| **Opt out** | `/wiki:session disable` makes trusted capture hooks no-ops; `/wiki:session enable` turns capture back on. |

```text
/wiki:session status
/wiki:session list --limit 10
/wiki:session show codex:abc123
/wiki:session rehydrate --cwd "$PWD"
/wiki:session promote codex:abc123 --topic meta-llm-wiki
/wiki:feedback list --unpromoted
/wiki:feedback promote fb-abc123 --topic meta-llm-wiki
```

This harness-session layer is distinct from `.research-session.json` and
`.thesis-session.json` crash recovery, and from `.session-events.jsonl` and
`.session-checkpoint.json` workflow provenance. See the
[session reference](claude-plugin/skills/wiki-manager/references/sessions.md)
for the storage layout, privacy defaults, capture modes, and adapter contract.

## Commands

| Command | Description |
|---------|-------------|
| `/wiki <natural language>` | Fuzzy intent router — say what you want and it routes to the right subcommand |
| `/wiki` | Show wiki status, stats, and list all topic wikis |
| `/wiki init <name>` | Create a topic wiki at `~/wiki/topics/<name>/` |
| `/wiki init <name> --local` | Create a project-local wiki at `.wiki/` |
| `/wiki:ingest <source>` | Ingest a URL, file path, PDF, or quoted text |
| `/wiki:ingest --inbox` | Process all files in the topic wiki's inbox/ |
| `/wiki:ingest-collection <source>` | Bulk-ingest Git doc repos, BIP-style proposal sets, MediaWiki dumps/API sites, message archives, or Wayback CDX snapshots |
| `/wiki:ingest-collection <source> --adapter git\|mediawiki-dump\|mediawiki-api\|csv-messages\|wayback-cdx` | Force a collection adapter |
| `/wiki:ingest-collection <source> --limit <N> --dry-run` | Preview or cap a large collection import |
| `/wiki:adapter add <local-path>` | Register an existing explicitly trusted private adapter checkout; never clones or publishes it |
| `/wiki:adapter list\|show\|doctor` | Inspect registrations and verify manifest/executable handshakes |
| `/wiki:adapter run <id> --request <json>` | Execute a scoped v1 request and verify artifacts without automatic wiki import; remote writes additionally require an exact approved plan hash and private verified receipt |
| `/wiki:adapter remove <id> --yes` | Remove only the machine-local registration, not adapter code or data |
| `/wiki:specialist init\|create\|refresh\|list\|show\|validate` | Manage personal, instruction-only specialist `SKILL.md` methods under the local hub at `HUB/.skills/` |
| `/wiki:specialist enable\|disable <name> --wiki <topic>` | Change the explicit per-active-topic specialist allowlist |
| `/wiki:specialist suggest [--wiki <topic\|all>]` | Rank bounded specialist methods justified by current wiki indexes without creating them |
| `/wiki:specialist apply <name> <question> --wiki <topic>` | Apply one enabled, validated specialist and report its version/hash |
| `/wiki:collect "<things>"` | Find, dedupe, and catalog artifacts, examples, resources, media, memes, tools, entities, or source candidates |
| `/wiki:collect "<things>" --scale tiny\|small\|medium\|large\|huge` | Control write behavior by operational scale, not just row count |
| `/wiki:collect "<things>" --media archive\|thumbnail\|reference` | Download/cache bounded originals by default; use thumbnail for previews or reference to opt out |
| `/wiki:collect "<things>" --inventory records` | Create per-item inventory records when the collected set is small enough to stay useful |
| `/wiki:collect "<things>" --inventory corpus` | Track a large, unstable, or media-heavy collection as one corpus record linked to the catalog output |
| `/wiki:inventory list` | List durable tracking records as compact chat-friendly tables or bullets |
| `/wiki:inventory list --view actions` | Show current inventory next actions without dumping full records |
| `/wiki:inventory add <kind> "title"` | Add an inventory record after checking that inventory is the right layer |
| `/wiki:inventory save-view "name"` | Save a derived reusable table/list under `inventory/views/` |
| `/wiki:inventory scan-outputs --dry-run` | Find old queue/backlog outputs and preview sample records before migration |
| `/wiki:inventory migrate-output <path> --apply` | Additively create inventory records from a legacy output; never moves or deletes the output |
| `/wiki:idea new [<slug>] "<seed>"` | Capture a rough proposal under `inventory/ideas/` without creating a Project |
| `/wiki:idea list\|show` | Browse the topic or hub-wide Idea catalog with derived maturity and next actions |
| `/wiki:idea develop\|shape <slug>` | Research an Idea, challenge assumptions, and prepare minimal/ideal shapes for approval |
| `/wiki:idea promote <slug>` | Explicitly promote an approved snapshot into a linked Project with `WHY.md` and frozen `BRIEF.md` |
| `/wiki:idea archive <slug>` | Archive the Idea record without implicitly archiving its linked Project |
| `/wiki:portfolio [filters]` | Show a read-only hub-wide view of canonical Ideas and active Projects without creating a catch-all topic |
| `/wiki:dataset list` | List dataset manifests as compact chat-friendly tables or bullets |
| `/wiki:dataset list --view schema` | Show schema/readiness state without opening samples or data |
| `/wiki:dataset add "title" --location <path-or-url>` | Add a dataset manifest without copying data into the wiki |
| `/wiki:dataset profile <slug> --dry-run` | Preview lightweight profiling of size, format, headers, or schema observations |
| `/wiki:dataset migrate-output <path> --apply` | Additively create dataset manifests from a legacy output; never moves or copies the underlying data |
| `/wiki:archive list [--archived]` | List active topic wikis and optionally archived topic wikis |
| `/wiki:archive topic <slug> --reason "why"` | Move a topic wiki to `topics/.archive/<slug>` and hide it from default context |
| `/wiki:archive restore <slug>` | Restore an archived topic wiki to active status |
| `/wiki:archive peek <query>` | Search archived topic indexes without reading archived articles |
| `/wiki:session status` | Show automated session-capture mode, root, and indexed session count |
| `/wiki:session disable` | Opt out of automated redacted session capture |
| `/wiki:session enable --mode balanced` | Re-enable or tune automated capture and soft rehydration |
| `/wiki:session capture` | Force a manual session digest checkpoint |
| `/wiki:session rehydrate` | Print compact context from matching session digests |
| `/wiki:session promote <id> --topic <slug>` | Promote a distilled digest into a topic raw note |
| `/wiki:feedback list --unpromoted` | Review high-signal user-feedback candidates captured from session hooks |
| `/wiki:feedback show <id>` | Inspect a candidate with distilled lesson, confidence, scope, and redacted preview |
| `/wiki:feedback promote <id> --topic <slug>` | Promote a selected feedback candidate into topic `raw/notes/` |
| `/wiki:compile` | Compile new sources into wiki articles |
| `/wiki:compile --full` | Recompile everything from scratch |
| `/wiki:query <question>` | Q&A against the wiki (standard depth) |
| `/wiki:query <question> --quick` | Fast answer from indexes only |
| `/wiki:query <question> --deep` | Thorough — reads everything, checks raw + sibling wikis |
| `/wiki:query <question> --include-archived` | Explicitly search/read archived material, with archived citations labeled |
| `/wiki:query <terms> --list` | Find content by keyword, tag, or category (replaces old `/wiki:search`) |
| `/wiki:query --resume` | Reload context after a session break — recent activity, stats, last-updated articles |
| `/wiki:plan <goal>` | Generate wiki-grounded implementation plan (interview → gap research → phased plan) |
| `/wiki:plan <goal> --quick` | Plan from wiki content only — skip interview and gap research |
| `/wiki:plan <goal> --format rfc\|adr\|spec` | Output as RFC, ADR, or tech spec instead of roadmap |
| `/wiki:research <topic>` | 5 parallel agents: academic, technical, applied, news, contrarian |
| `/wiki:research <topic> --new-topic` | Create a topic wiki and start researching — works from any directory |
| `/wiki:research <topic> --min-time 1h` | Keep researching in rounds until time budget is spent |
| `/wiki:research <topic> --plan` | Decompose into 3-5 parallel paths, confirm, then dispatch all at once |
| `/wiki:research <topic> --specialist <name>` | Apply an enabled personal specialist method; repeat at most three times |
| `/wiki:research <topic> --no-specialists` | Run the baseline workflow without loading specialist bodies |
| `/wiki:research <topic> --deep` | 8 agents: adds historical, adjacent, data/stats |
| `/wiki:research <topic> --retardmax` | 10 agents: skip planning, max speed, ingest aggressively |
| `/wiki:thesis <claim>` | Thesis-driven research: evidence for + against → verdict |
| `/wiki:thesis <claim> --min-time 1h` | Multi-round thesis investigation with anti-confirmation-bias |
| `/wiki:lint` | Run health checks on the wiki |
| `/wiki:lint --fix` | Auto-fix structural issues |
| `/wiki:lint --deep` | Web-verify facts and suggest improvements |
| `/wiki:audit` | Umbrella trust audit: wiki, outputs, provenance, and fresh research when needed |
| `/wiki:audit --artifact <path>` | Audit one article or output artifact and follow its evidence chain |
| `/wiki:audit --project <slug>` | Audit one project's outputs and upstream wiki state |
| `/wiki:audit report` | Display the latest umbrella audit report |
| `/wiki:librarian` | Focused wiki maintenance: staleness and quality scan for the `wiki/` layer |
| `/wiki:librarian --article <path>` | Scan a single article |
| `/wiki:librarian scan --passes staleness,quality,conventions` | Generate topic-guide advice/proposals for established wikis without rewriting `schema.md` |
| `/wiki:librarian report` | Display the latest librarian scan report |
| `/wiki:refresh [<article-path>|--due]` | Re-check article sources for changed facts and offer human-gated updates |
| `/wiki:output <type>` | Generate: summary, report, study-guide, slides, timeline, glossary, comparison |
| `/wiki:output <type> --retardmax` | Ship it now — rough but comprehensive, iterate later |
| `/wiki:checkpoint create [<slug>] --repo <path> --audience private\|team\|public` | Preview a comprehensive cross-topic checkpoint with source access, section coverage, detail-floor, privacy, and gap review |
| `/wiki:checkpoint create ... --apply` | Stage, synthesize, deterministically privacy-seal, verify, and write a five-file repo handoff without committing or pushing |
| `/wiki:checkpoint refresh <bundle> [--apply]` | Re-run stored scope and review source/claim/privacy differences before replacing generated files |
| `/wiki:checkpoint verify <bundle>` | Recheck structure, checkpoint/file hashes, privacy findings, and exact recorded overrides |
| `/wiki:checkpoint import <bundle\|repo> --wiki <name>` | Verify and ingest a pinned checkpoint as bounded source evidence, never canonical truth |
| `/wiki:project new <slug> "goal"` | Group related outputs under `output/projects/<slug>/` with a plain `WHY.md` rationale |
| `/wiki:project list\|show\|add\|archive` | Manage output project folders without duplicating project state into frontmatter |
| `/wiki:retract [<source-path>]` | User-authoritative removal of a source and its downstream wiki references, including selected archives and sessions |
| `scripts/llm-wiki retract --everywhere [--apply]` | Secret-safe local value scan: hidden/stdin input, common encoded forms, dry-run first, then apply and verify |
| `/wiki:ll` | Extract lessons learned from the current session into the wiki |
| `/wiki:ll --dry-run` | Preview extracted lessons without writing |
| `/wiki:ll --rules` | Also suggest CLAUDE.md / AGENTS.md rule additions |
| `/wiki:assess <path>` | Assess a repo against wiki research + market. Gap analysis. |
| `/wiki:assess <path> --retardmax` | Wide net — adds adjacent fields and failure analysis |

All commands accept `--wiki <name>` to target a specific topic wiki and `--local` to target the project wiki. Archived topic wikis are skipped by default; commands that support `--include-archived` require that explicit flag before reading or writing archived material. Retraction is the exception: an explicitly selected archived target needs no additional gate, and `scripts/llm-wiki retract --everywhere` includes archives and session context. Commands that generate content (`query`, `output`, `plan`) also accept `--with <wiki>` to load supplementary wikis as cross-wiki context — e.g., `--with article-writing` applies writing craft knowledge when generating output from a domain wiki.

`/wiki:librarian` is the focused wiki-maintenance tool. `/wiki:audit` is broader and may perform fresh research to decide whether the current knowledge or generated outputs are still trustworthy.

## How It Works

### Architecture

```
~/wiki/                                 # Hub — lightweight, no content
├── wikis.json                          # Registry of all topic wikis
├── _index.md                           # Lists topic wikis with stats
├── log.md                              # Global activity log
├── .sessions/                          # Optional session capture + feedback candidates
├── .skills/                            # Optional personal specialist methods + topic allowlists
└── topics/                             # Each topic is an isolated wiki
    ├── nutrition/                      # Example topic wiki
    │   ├── .obsidian/                  # Optional Obsidian vault config
    │   ├── inbox/                      # Drop zone for this topic
    │   ├── inventory/                  # Lazy: durable records, Ideas, and derived views
    │   ├── datasets/                   # Lazy: manifests for large/external data
    │   ├── raw/                        # Immutable sources
    │   ├── wiki/                       # Compiled articles
    │   │   ├── concepts/
    │   │   ├── topics/
    │   │   └── references/
    │   ├── output/                     # Generated artifacts
    │   ├── _index.md
    │   ├── config.md
    │   ├── schema.md                  # Human-owned topic guide
    │   └── log.md
    ├── woodworking/                    # Another topic wiki
    ├── .archive/                       # Archived topic wikis, hidden by default
    └── ...
```

The hub has no content directories or `.obsidian/`; optional `.sessions/` and
`.skills/` are operational configuration/memory layers. All content lives in
topic sub-wikis with isolated indexes, articles, and a human-owned advisory
topic guide (`schema.md`). Init creates the core wiki skeleton first; optional
inventory and dataset layers are created when you use them. Queries stay
focused. The multi-wiki peek finds overlap across topics when relevant.

### The Flow

1. **Research** a topic — parallel agents search the web, ingest sources, and compile articles in one command
2. **Apply specialist methods** — select a topic-allowlisted evidence/review protocol without pretending the model holds a credential
3. **Ingest** additional sources — URLs, files, text, tweets (via Grok MCP), or bulk via inbox
4. **Collect** catalogs of discoverable things — examples, media, memes, tools, projects, entities, or source candidates — then optionally inventory them
5. **Inventory** items, candidates, entities, corpora, watch lists, and next actions that should persist; the agent tells you when inventory is the wrong layer
6. **Develop Ideas** from rough seed to researched, challenged, approved shape, then explicitly promote them into delivery Projects
7. **Index datasets** that are too large for markdown — manifests, profiles, samples, and query recipes
8. **Archive** whole topic wikis that should stay preserved but quiet
9. **Compile** raw sources into synthesized wiki articles with cross-references and confidence scores
10. **Query** the wiki — quick (indexes), standard (articles), or deep (everything active, archived indexes separated)
11. **Session capture** — automatically preserve redacted Codex/Claude/OpenCode/Gemini checkpoints under `.sessions/` and rehydrate future turns
12. **Feedback curator** — capture reviewable correction/preference/approval candidates under `.sessions/feedback/` and promote only what matters
13. **Lessons learned** — extract knowledge from the current session (errors, fixes, gotchas) into the wiki
14. **Assess** a repo against the wiki — gap analysis: what aligns, what's missing, what the market offers
15. **Lint** for consistency — broken links, missing indexes, orphan articles, archive registry drift
16. **Output** artifacts — summaries, reports, slides — filed back into the wiki

### Key Design

- **One topic, one wiki** — each research area gets its own sub-wiki with isolated indexes. No cross-topic noise.
- **Canonical collection slugs** — collection families use kind-first topic
  names such as `memes-bitcoin`, `memes-ethereum`, or `tools-bitcoin` so
  related catalogs group naturally as the hub grows.
- **Parallel research agents** — 5 standard, 8 deep, 10 retardmax. Each agent searches from a different angle.
- **Personal specialist methods** — user-owned, instruction-only `SKILL.md`
  protocols selected by task features and enabled per topic; methods, not
  credential costumes.
- **Collector workflow** — search-driven catalogs for objects, media, and
  examples; saves a provenance map first, then inventories only the durable
  subset.
- **Concept → Idea → Project** — compiled Concepts hold knowledge, cataloged
  Ideas hold researched/shaped proposals, and Projects begin only after
  explicit delivery commitment. Natural language routes the whole lifecycle.
- **Hub-wide portfolio** — one live, read-only view cross-references distributed
  Ideas and direct/promoted Projects without duplicating topic-owned records.
- **`_index.md` navigation** — every existing wiki-managed directory has an index. Claude reads indexes first, never scans blindly.
- **Articles are synthesized**, not copied — they explain, contextualize, cross-reference.
- **Raw is immutable in normal workflows** — explicit user-directed retraction is the exception and removes selected raw and derived references.
- **Multi-wiki aware** — queries peek at sibling wiki indexes for overlap.
- **Archive-aware** — archived topic wikis stay preserved under
  `topics/.archive/` but are hidden from default query/compile/research/collect/output
  and maintenance workflows.
- **Dual-linking** — both `[[wikilinks]]` (Obsidian) and standard markdown links on every cross-reference. Works everywhere.
- **Confidence scoring** — articles rated high/medium/low based on source quality and corroboration.
- **Structural guardian** — auto-checks wiki integrity after operations, fixes trivial issues silently.
- **Activity log** — `log.md` tracks every operation, append-only, grep-friendly.
- **Opinionated inventory** — durable tracking gets records; one-off sources stay
  ingest/query; large row-like data becomes datasets or collection ingests. Big
  pivots start with a sample table before records are written.
- **Media-safe catalogs** — bounded public binary media is cached under
  `output/assets/collect-<slug>/` by default; raw sources remain textual
  evidence, and large media sets become dataset manifests. Bulk downloads use
  timeouts, file-size caps, content-type checks, and IPv4 retry when needed.
- **Feedback is candidate memory** — corrections, preferences, approvals, and
  plan acceptance are saved as redacted candidates under `.sessions/feedback/`;
  generic acknowledgements are ignored, and promotion into topic notes is
  explicit.
- **Zero dependencies** — runs entirely on built-in tools (Claude Code, OpenCode, or Codex).

## Research Modes

| Mode | Flag | Agents | Style |
|------|------|--------|-------|
| Standard | *(default)* | 5 | Academic, technical, applied, news, contrarian |
| Deep | `--deep` | 8 | Adds historical, adjacent fields, data/stats |
| Retardmax | `--retardmax` | 10 | Adds rabbit-hole agents. Skip planning, cast widest net, ingest aggressively, compile fast. Lint later. |

**Smart input detection** — `/wiki:research` auto-detects whether you're passing a topic or a question:

| Input | Detected as | Behavior |
|-------|-------------|----------|
| `"nutrition"` | Topic | Standard research — explore the field |
| `"What makes articles go viral?"` | Question | Decompose into sub-questions → one agent per sub-question → synthesize → generate playbook → suggest theses |

Question mode produces a **playbook** (actionable output artifact) and suggests **testable theses** derived from the findings.

**Modifiers** (combine with any mode):

| Flag | What it does |
|------|-------------|
| `--new-topic` | Create a topic wiki from the research topic and start immediately. Works from any directory. |
| `--plan` | Decompose into 3-5 parallel research paths, confirm, then dispatch all paths simultaneously. Parallel ingest, sequential compile. |
| `--min-time <duration>` | Keep running research rounds until the time budget is spent (`30m`, `1h`, `2h`, `4h`). Each round drills into gaps the previous round found. |
| `--sources <N>` | Sources per round (default: 5, retardmax: 15) |

```
# The full combo — new topic, 2 hours of deep research, from anywhere
/wiki:research "CRISPR gene therapy" --new-topic --deep --min-time 2h
```

Retardmax mode is inspired by [Elisha Long's retardmaxxing philosophy](https://www.retardmaxx.com/) — act first, think later. The antidote to analysis paralysis. Works for both `/wiki:research` and `/wiki:output`.

## Thesis-Driven Research

Unlike open-ended research, `/wiki:thesis` starts with a specific claim and evaluates it:

```
/wiki:thesis "intermittent fasting reduces neuroinflammation via glymphatic upregulation"
```

**How it works:**
1. Decomposes the thesis into key variables, testable predictions, and falsification criteria
2. Launches parallel agents — but each agent has the thesis as a FILTER. Irrelevant sources get skipped (this prevents bloat)
3. Agents are split: **supporting**, **opposing**, **mechanistic**, **meta/review**, **adjacent** — balanced by design
4. Compiles evidence into wiki articles + a thesis file with evidence tables
5. Delivers a **verdict**: supported / partially supported / contradicted / insufficient evidence / mixed

**Anti-confirmation-bias**: When using `--min-time`, Round 2 automatically focuses harder on the WEAKER side of the evidence. If Round 1 found mostly supporting evidence, Round 2 hunts for counter-evidence.

**The thesis is the bloat filter.** Sources that don't relate to the claim's variables don't get ingested. Higher skip rate = tighter focus.

## Linking: Works Everywhere

Every cross-reference in the wiki uses dual-link format:

```markdown
[[gut-brain-axis|Gut-Brain Axis]] ([Gut-Brain Axis](../concepts/gut-brain-axis.md))
```

The wiki is **not locked into any tool**:

- **Obsidian** reads the `[[wikilink]]` — graph view, backlinks panel, quick-open
- **Claude Code** follows the standard `(relative/path.md)` link
- **GitHub/any markdown viewer** renders the standard link as clickable
- **No viewer at all** — plain markdown, readable in any text editor

## Obsidian Integration

Each topic wiki has its own `.obsidian/` config and can be opened as an independent vault:

```
open ~/wiki/topics/nutrition/     # Open in Obsidian — focused graph for one topic
```

The hub (`~/wiki/`) has no `.obsidian/` to avoid nested vault confusion. If you want a cross-topic view, open `~/wiki/` manually and let Obsidian create its own config.

What works out of the box:

- `.obsidian/` config can be created on init with sane defaults
- `[[wikilinks]]` power the graph view
- `aliases` in frontmatter enable search by alternate names
- `tags` in frontmatter are natively read
- `inbox/` works as a drop zone in both Obsidian and the CLI

Claude Code is the compiler. Obsidian is an optional viewer.

## Query Depths

| Depth | Flag | What it does |
|-------|------|-------------|
| Quick | `--quick` | Reads indexes only. Fastest. For simple lookups. |
| Standard | *(default)* | Reads relevant articles + full-text search. For most questions. |
| Deep | `--deep` | Reads everything active, searches raw sources, peeks sibling wikis, and surfaces archived index matches separately. |
| List | `--list` | Returns ranked article list instead of synthesized answer. Supports `--tag` and `--category` filters. |

Archived topics are excluded from quick, standard, and list results unless you
pass `--include-archived`. Deep mode may show archived index hits, but it does
not cite archived material as active evidence without explicit inclusion.

## Development Benchmarks

Token-efficiency changes are tested with deterministic context budgets and
optional real Codex and Claude Code AB/BA harnesses. See
[`benchmarks/README.md`](benchmarks/README.md) for commands, quality gates, and
cache-metric caveats.

## Credits

- [Andrej Karpathy](https://x.com/karpathy) — the [LLM wiki concept](https://x.com/karpathy/status/2039805659525644595) and [idea file](https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f)
- [Elisha Long](https://www.retardmaxx.com/) — retardmaxxing philosophy (act first, think later)
- [tobi/qmd](https://github.com/tobi/qmd) — recommended local search engine for scaling beyond ~100 articles
- [rvk7895/llm-knowledge-bases](https://github.com/rvk7895/llm-knowledge-bases) — prior art in Claude Code wiki plugins

## License

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files, to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, subject to the following conditions: the above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

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