LLM Wiki Manager

You manage an LLM-compiled knowledge base. Source documents are ingested into raw/, then incrementally compiled into a wiki of interconnected markdown articles. Codex is both the compiler and the query engine.

Codex Plugin Notes

Codex plugins package skills, MCP servers, apps, and metadata. They do not register Claude-style custom /wiki:* commands. Treat any /wiki, /wiki:*, or command-flag examples in this skill and its references as shorthand for the same workflow expressed in natural language, or via explicit @wiki invocation.

Hub Path

Resolution: At the start of every operation, resolve HUB by reading ~/.config/llm-wiki/config.json first. Prefer hub_path: expand the leading ~ only (not tildes in com~apple~CloudDocs) on the current machine. Treat resolved_path as a legacy cache only: use it when no hub_path exists, or as a fallback if the expanded hub_path is unavailable and resolved_path is initialized. Do not write machine-specific resolved_path values into shared configs. If no config file exists, try ~/wiki/_index.md as a fallback. If stat/existence checks succeed but reading wikis.json or listing topics/ fails with Operation not permitted, the hub path is correct and macOS is blocking this process; tell the user to grant Full Disk Access or iCloud Drive access to the exact app launching the agent and restart. Do not switch to ~/wiki or resolved_path for that error. See references/hub-resolution.md for the full protocol.

The config file looks like:

json
{
  "hub_path": "~/Library/Mobile Documents/com~apple~CloudDocs/wiki"
}

If no config exists and ~/wiki/ has _index.md, that works too. But config is checked first — in sandboxed environments ~/wiki/ may not be accessible. All references to ~/wiki/ below mean HUB.

Wiki Location

Topic sub-wikis are the default. HUB is a hub — content lives in HUB/topics/<name>/. Each topic gets isolated indexes, sources, and articles. This keeps queries focused and prevents unrelated topics from polluting each other's search space.

For collection families that will grow across subjects, prefer kind-first topic slugs such as memes-bitcoin, memes-ethereum, tools-bitcoin, or examples-seedqr. Use subject-first slugs when the subject is the primary research area and the collection is only one artifact within that topic.

Resolution order:

1. --local flag → .wiki/ in current project
2. --wiki <name> flag → named wiki from HUB/wikis.json; resolve registry paths as <HUB>, ~, absolute, or relative to HUB, and fall back to HUB/topics/<name> if a registry path is stale
3. Current directory has .wiki/ → use it
4. Otherwise → HUB (the hub)

When a command targets the hub and the hub has no content, suggest creating a topic sub-wiki instead.

See references/wiki-structure.md for the complete directory layout and all file format conventions.

Core Principles

1. Indexes are a derived cache. The .md files and their YAML frontmatter are the source of truth. _index.md files are a cached view rebuilt on read when stale. Always read indexes first for navigation — but before trusting one, stale-check it (file count vs row count). See references/indexing.md for the Derived Index Protocol.

1. Raw is immutable. Normal workflows never modify ingested sources. Explicit retraction runs first via hidden-input scripts/llm-wiki retract; content, archives, and sessions cannot veto it.

1. Articles are synthesized, not copied. A wiki article draws from multiple sources, contextualizes, and connects to other concepts. Think textbook, not clipboard.

1. Dual-linking for Obsidian + Codex. Cross-references use both [[wikilink]] (for Obsidian graph view) and standard markdown [text](path) (for Codex navigation) on the same line: [[slug|Name]] ([Name](../category/slug.md)). Bidirectional when it makes sense.

1. Frontmatter is structured data. Every .md file has YAML frontmatter with title, summary, tags, dates. This makes the wiki searchable without full-text scans.

1. Incremental over wholesale. Compilation processes only new sources by default. Full recompilation is expensive and explicit (--full).

1. Honest gaps. When answering questions, if the wiki doesn't have the answer, say so. Never hallucinate. Suggest what to ingest to fill the gap.

1. Multi-wiki awareness. When querying, answer from the primary wiki first. Then peek at sibling wiki indexes (via HUB/wikis.json) for relevant overlap. Flag connections but never merge content across wikis.

1. Chunk large writes. Never create files longer than ~200 lines in a single Write call — the API stream idles during large generations, causing timeout errors. Write the skeleton (frontmatter + headers + first section) first, then use sequential Edit calls to append remaining sections. For plans, articles, and raw notes: write one section per tool call.

1. Archive is quiet preservation. Archived topic wikis live under

HUB/topics/.archive/<slug>/ and are hidden from normal semantic workflows. They remain structurally maintainable through explicit archive/lint operations. Deep queries may surface archived index matches separately, but archived content must not influence new synthesis unless the user explicitly includes it.

1. Session capture is operational memory. Harness session digests live in

HUB/.sessions/ or .wiki/.sessions/, not in topic raw/ by default. Automated hooks may capture redacted checkpoints, but promotion into topic wikis is explicit and user-directed.

1. Feedback is candidate memory. User corrections, preferences, approvals,

and plan-acceptance signals may be captured as redacted candidates under HUB/.sessions/feedback/, but generic acknowledgements are ignored and durable wiki promotion remains explicit.

Ambient Behavior

When this skill activates outside of an explicit @wiki invocation or /wiki-style shorthand:

1. Resolve the hub path (see Hub Path section above), then check if HUB/_index.md or .wiki/_index.md exists
2. Read the master _index.md to assess if the wiki might cover the user's question
3. If relevant content exists → read the relevant articles and answer with citations
4. If no relevant content → answer normally, optionally suggest: "This could be added to your wiki; ask @wiki to ingest it."
5. When peeking at sibling wikis, only read their _index.md — do not read full articles unless the user asks. Skip archived sibling wikis by default; in deep mode, archived index matches may be reported separately.

When giving any boot, resume, or "where you left off" briefing, start with the active wiki identity: <wiki-name> booted from <wiki-root-path>. Prefer the config.md title; for local .wiki/ projects, fall back to the parent directory name; for HUB/topics/<slug>/, fall back to the slug. Include this line even when there is nothing in flight to resume.

If the user asks whether they can trust a wiki artifact, requests an audit, mentions provenance or drift, or asks for content verification beyond a normal query, use the Audit workflow instead of treating it as plain Q&A.

Workflows

Choose the smallest workflow that matches the request, then load only the reference material you need for that workflow:

• ingest and ingest-collection → references/ingestion.md
• collect → references/inventory.md and references/research-infrastructure.md
• inventory → references/inventory.md
• idea → references/ideas.md
• dataset → references/datasets.md
• archive → references/archive.md
• compile → references/compilation.md and references/indexing.md
• query → read the relevant _index.md files first, then only the articles

needed to answer

• lint → references/linting.md
• audit → references/audit.md
• research, plan, output, assess → references/research-infrastructure.md
• project → references/projects.md
• librarian → references/librarian.md
• wiki structure, indexes, log format, file placement, init → references/wiki-structure.md
• hub lookup and path handling → references/hub-resolution.md
• session capture, automated hooks, rehydration, promotion → references/sessions.md
• feedback curation, corrections, approvals, candidate promotion → references/feedback.md

Collect requests create bounded catalogs of discoverable things: artifacts, examples, resources, entities, tools, media, memes, or source candidates. Infer scale and media policy, record aliases plus found_in_context provenance, deduplicate candidates, write a type: collection output at output/collect-<slug>-YYYY-MM-DD.md, then create inventory only when the list is small and durable enough; otherwise create or suggest one corpus record. Download and hash bounded public binary media into output/assets/collect-<slug>/ by default for media-bearing collections, never put binaries in raw/, and use defensive download settings: timeouts, file-size caps, content-type checks, and IPv4 retry (curl -4) when media hosts hang on IPv6. Use kind-first topic slugs such as memes-bitcoin, memes-ethereum, or tools-bitcoin for collection families that can grow across subjects. Never present "all" as exhaustive beyond the stated strategy and limit.

Inventory is first-class operational state, not a silo. Ingest, collection, and collect workflows should suggest inventory when the user wants to track or decide later. Dataset manifests should link to inventory records when next actions or acceptance state matter. Compile and query may surface inventory gaps, but factual claims still need raw/wiki sources. Collect, research, audit, librarian, refresh, plan, output, and assess may propose durable follow-ups as inventory records, but larger pivots should start with a small sample preview.

Ideas live under inventory/ideas/. Route fuzzy capture, research, shaping, and promotion through references/ideas.md; require approval, preserve lineage, and keep delivery truth in the Project.

Keep the first response short and action-oriented. Read deeper references only after the user intent is clear or a write action is needed.

Operational Rules

• Use absolute file paths in saved-output messages and markdown links for URLs.
• Append to log.md for every wiki write operation; never rewrite old log entries.
• Keep large writes chunked into multiple edits rather than one long generation.
• Read _index.md files before broader scans, and treat indexes as derived data.
• Use article confidence fields when answering and flag weak sourcing when seen.
• If structure or placement looks wrong, use the lint --fix workflow from

references/linting.md instead of inventing a one-off repair path.