Harness session capture/rehydration/feedback

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LLM-compiled knowledge bases for any AI agent. Parallel multi-agent research, collector catalogs, automated session capture, feedback curation, thesis-driven investigation, source ingestion, wiki compilation, truth-seeking audits, querying, and artifact generation. Ships as a Claude Code plugin, an OpenAI Codex plugin, an OpenCode instruction file, or a portable AGENTS.md for any other LLM agent. Obsidian-compatible.

Install · Quick Start · Sessions · Commands · How It Works · Research Modes · Thesis Research · Query Depths · Linking · Obsidian · Architecture · Nono Sandbox · Upgrade · Changelog · Credits

v0.16.0 — Query Lite and token benchmarks. Adds a compact read-only query protocol across Claude Code, Codex, Pi, DS4, OpenCode, and portable agents; reduces Claude /wiki:query

instructions by 72.54%; adds explicit $wiki-query

, read-only Pi launchers, static context budgets, corpus-identity gates, and reproducible Codex/Claude/DS4 benchmark lanes. OpenCode live-model behavior remains best effort.

v0.15.0 — Topic guides. Reframes schema.md

as a human-owned topic guide, adds the friendlier llm-wiki schema adopt

helper, keeps schema migrate --apply

as a compatibility alias, and updates librarian docs to talk about conventions proposals instead of database-style schema migrations.

v0.14.0 — Default topic guides. Adds advisory schema.md

by default, safe adoption helpers for older wikis, proposal-only librarian convention updates, deterministic docs/lint checks, and clarifies the optional index/server layer as a rebuildable non-authoritative cache.

v0.12.0 — Feedback curator. Captures high-signal corrections, preferences, approvals, and plan acceptance as redacted feedback candidates under HUB/.sessions/feedback/

; ignores generic acknowledgements; adds review/manual-capture/promotion workflows; and keeps promotion into topic raw/notes/

explicit.

v0.11.1 — Session helper compatibility. Small hotfix so automated session capture works on Python 3.9/macOS system Python as well as newer Python runtimes.

v0.11.0 — Automated session capture. Default-on redacted checkpoints under HUB/.sessions/

, opt-out via session disable

, compact context rehydration, explicit digest promotion, and a tested Codex hook bundle.

Claude Code (native plugin):

claude plugin install wiki@llm-wiki

OpenAI Codex (marketplace plugin):

Install from GitHub:

codex plugin marketplace add nvk/llm-wiki
codex plugin add wiki@llm-wiki

Install from a local checkout with the managed bootstrap helper:

./scripts/bootstrap-codex-plugin.sh --scope user --verify

Or register the local checkout manually:

codex plugin marketplace add /absolute/path/to/llm-wiki
codex plugin add wiki@llm-wiki

Canonical explicit invocation:

$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:

codex plugin marketplace upgrade llm-wiki
codex plugin add wiki@llm-wiki

Remove:

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

, seeNono 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):

{
  "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:

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:

{
  "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:

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:

./scripts/pi-wiki-query

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

./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:

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 and the reproducible

DS4 lane.

benchmarks/README.md

Any LLM Agent (portable instruction file):

cp profiles/query-lite/SKILL.md ~/your-project/AGENTS.md

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 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 generatedwiki-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:

./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.

If you run any AI coding agent inside a nono sandbox, the wiki needs filesystem access beyond the default profile.

{
  "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 needs r+w to its own $HOME/.codex

directory for plugin install, marketplace cache, state, and skill registration:

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

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 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:

/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.

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:

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) — nono and OpenCode have independent sandboxes that both need the same paths allowed.

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:

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

Claude Code — if claude plugin update

pulls the latest correctly:

git -C ~/.claude/plugins/marketplaces/llm-wiki remote set-url origin https://github.com/nvk/llm-wiki.git
claude plugin update wiki@llm-wiki

If the update command doesn't pick up the new version (stale marketplace cache), sync manually from the repo:

git clone https://github.com/nvk/llm-wiki.git  # or: git -C ~/llm-wiki pull

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/"

Codex — upgrade from the marketplace:

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:

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:

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.

/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: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: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:

./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

This local helper covers structural checks and safe migrations that do not require an LLM. 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.

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.

/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 for the storage layout, privacy defaults, capture modes, and adapter contract.

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
Force a collection adapter
/wiki:ingest-collection <source> --limit <N> --dry-run
Preview or cap a large collection import
/wiki:collect "<things>"
Find, dedupe, and catalog artifacts, examples, resources, media, memes, tools, entities, or source candidates
`/wiki:collect "<things>" --scale tiny	small
Control write behavior by operational scale, not just row count
`/wiki:collect "<things>" --media archive	thumbnail
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: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
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> --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 [	--due]`
/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:project new <slug> "goal"
Group related outputs under output/projects/<slug>/ with a plain WHY.md rationale
`/wiki:project list	show
Manage output project folders without duplicating project state into frontmatter
/wiki:retract <source-path> --reason "why"
Remove a bad source, map blast radius, and flag downstream claims for review
/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. 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.

~/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
└── 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 tracking records + 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 is just a registry — no content directories, no .obsidian/

. 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.

Research a topic — parallel agents search the web, ingest sources, and compile articles in one commandIngest additional sources — URLs, files, text, tweets (via Grok MCP), or bulk via inboxCollect catalogs of discoverable things — examples, media, memes, tools, projects, entities, or source candidates — then optionally inventory themInventory items, candidates, entities, corpora, watch lists, and next actions that should persist; the agent tells you when inventory is the wrong layerIndex datasets that are too large for markdown — manifests, profiles, samples, and query recipesArchive whole topic wikis that should stay preserved but quietCompile raw sources into synthesized wiki articles with cross-references and confidence scoresQuery the wiki — quick (indexes), standard (articles), or deep (everything active, archived indexes separated)Session capture— automatically preserve redacted Codex/Claude/OpenCode/Gemini checkpoints under.sessions/

and rehydrate future turnsFeedback curator— capture reviewable correction/preference/approval candidates under.sessions/feedback/

and promote only what mattersLessons learned— extract knowledge from the current session (errors, fixes, gotchas) into the wiki** Assessa repo against the wiki — gap analysis: what aligns, what's missing, what the market offers Lintfor consistency — broken links, missing indexes, orphan articles, archive registry drift Output**artifacts — summaries, reports, slides — filed back into the wiki

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 asmemes-bitcoin

,memes-ethereum

, ortools-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.** Collector workflow**— search-driven catalogs for objects, media, and examples; saves a provenance map first, then inventories only the durable subset.— every existing wiki-managed directory has an index. Claude reads indexes first, never scans blindly._index.md

navigationArticles are synthesized, not copied — they explain, contextualize, cross-reference.** Raw is immutable**— once ingested, sources are never modified.** Multi-wiki aware**— queries peek at sibling wiki indexes for overlap.** Archive-aware**— archived topic wikis stay preserved undertopics/.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 underoutput/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).

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)

/wiki:research "CRISPR gene therapy" --new-topic --deep --min-time 2h

Retardmax mode is inspired by Elisha Long's retardmaxxing philosophy — act first, think later. The antidote to analysis paralysis. Works for both /wiki:research

and /wiki:output

.

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:

• Decomposes the thesis into key variables, testable predictions, and falsification criteria
• Launches parallel agents — but each agent has the thesis as a FILTER. Irrelevant sources get skipped (this prevents bloat)
• Agents are split: supporting,** opposing**,** mechanistic**,** meta/review**,** adjacent**— balanced by design - Compiles evidence into wiki articles + a thesis file with evidence tables
• 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.

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

[[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-openClaude Code follows the standard(relative/path.md)

linkGitHub/any markdown viewer renders the standard link as clickableNo viewer at all— plain markdown, readable in any text editor

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 viewaliases

in frontmatter enable search by alternate namestags

in frontmatter are natively readinbox/

works as a drop zone in both Obsidian and the CLI

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

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.

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

Andrej Karpathy— theLLM wiki conceptandidea fileElisha Long— retardmaxxing philosophy (act first, think later)tobi/qmd— recommended local search engine for scaling beyond ~100 articlesrvk7895/llm-knowledge-bases— prior art in Claude Code wiki plugins

MIT License. Copyright (c) 2026 nvk.

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.

source & further reading

github.com — original article