Wiki Manager

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. Claude Code is both the compiler and the query engine — no Obsidian, no external tools.

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:

{
  "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.

2. 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.

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

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

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

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

7. 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.

8. 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.

9. 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.

10. 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.

11. 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.

12. 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.

13. Private adapters are a content-free external execution plane. Their machine-local registry lives under ~/.config/llm-wiki/, not in the hub. Adapter repositories contain tool code only; real inputs and all runtime outputs remain in separately controlled external data planes. Only reviewed wiki-safe candidates may enter the wiki through normal provenance and compilation workflows. See references/adapters.md.

14. Specialists are bounded methods, not credentials. Personal, instruction-only specialist packages live locally under HUB/.skills/ and are enabled per active topic. Loading one never grants tools, write access, professional authority, or permission to spawn agents. Select the minimum useful method, preserve disagreement, and record its version/hash. See references/specialists.md.

15. Project checkpoints need comprehensive coverage and a privacy seal. See references/checkpoints.md.

Adapter Routing

For an action plus URL, run adapter route --intent <effect> --resource <url> --json before ingestion or generic tool advice, even when the user did not say "wiki." On a match, read its adapter-owned guide; provider steps live there. A URL alone is not write authorization. See references/adapters.md.

Explicit wiki skill-factory <request> selects the registered named adapter; do not invent a URL route. Run show/doctor and read its guide. It never activates ambiently, and its external candidates remain disabled; installation, topic enablement, commit, and publication are separate actions.

Ambient Behavior

When this skill activates outside of an explicit /wiki:* command:

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 with /wiki:ingest"
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

Ingestion

See references/ingestion.md. Flow: Source (URL/file/text/tweet/inbox) → fetch/read → extract metadata → write to raw/{type}/ → update indexes → suggest compile if many uncompiled.

Collection Ingestion

See references/ingestion.md § Collection Ingestion. Flow: structured upstream collection (Git repo, BIP-style proposal set, MediaWiki dump/API) → upstream item inventory → write a raw/repos/ manifest plus immutable child sources → rebuild raw indexes → optionally compile synthesized clusters. Use /wiki:ingest-collection for bulk imports; never recursively crawl HTML.

Private Adapters

See references/adapters.md. Flow: explicitly register an existing local adapter checkout → declare read and write roots → verify the manifest hash and describe handshake → execute a v1 JSON request through the bundled deterministic CLI → verify artifact paths and hashes → leave all outputs external → optionally review only wiki-safe candidates and promote the smallest useful evidence through normal wiki writes. If the guide offers an agent-started interactive authorization helper, launch it yourself and present only its short local handoff link rather than a long terminal command or provider URL. Never clone, install, update, publish, or auto-promote an adapter.

Personal Specialist Skills

See references/specialists.md. Flow: maintain user-owned instruction-only SKILL.md methods under HUB/.skills/ → validate structure and safety boundaries → explicitly enable stable names per active topic → select zero to three by task features, normally one → give selected methods the same bounded evidence packet → verify and synthesize by evidence strength → record name, version, and content hash. Use /wiki:specialist suggest for an index-first candidate scan and /wiki:specialist apply for a bounded review. Do not treat titles such as CFO, doctor, MBA, or PhD as credentials or capability upgrades.

Inventory

See references/inventory.md. Flow: Run an inventory fit check → track durable wiki-adjacent things (items, Ideas, ingest candidates, entities, corpora, questions, tasks, watch items) as markdown records under inventory/ → answer list requests from indexes/frontmatter as compact chat tables or bullets → optionally save derived views under inventory/views/ → optionally convert legacy queue-like outputs through explicit dry-run-first migration. Inventory migration is additive and human-gated. Be explicit when something is too small for inventory, too large and should be a dataset/collection, or outside wiki scope.

Ideas

See references/ideas.md. Flow: capture in inventory/ideas/ → research/shape → require approval → freeze BRIEF.md and promote. The Idea keeps lineage; the Project owns delivery.

Portfolio

See references/portfolio.md. Flow: read active Idea indexes and Project WHY.md files → cross-link only explicit lineage → render separate read-only tables without copying records.

Collect

See references/inventory.md and references/research-infrastructure.md. Flow: Scope a bounded catalog request → infer scale and media policy → search for candidate artifacts, examples, resources, entities, tools, media, or memes → fetch only promising context pages → deduplicate aliases/reposts/rehosts → record found_in_context provenance and media metadata → save a type: collection output under output/collect-<slug>-YYYY-MM-DD.md → optionally create inventory records when the list is small and durable enough, or one corpus record when it is medium/large. Collect outputs are useful to the LLM as a staging layer before promotion into raw/, wiki/, inventory, or datasets; they do not replace raw sources for factual claims. Download and hash bounded public binary media into output/assets/collect-<slug>/ by default for media-bearing collections, never store 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. Do not pretend that "all" means exhaustive beyond the stated strategy and limit.

Dataset Registry

See references/datasets.md. Flow: Keep large or external datasets out of the wiki while indexing them through datasets/<slug>/MANIFEST.md → store locations, schema notes, small samples, profiles, and query recipes → answer list requests from datasets/_index.md plus manifest frontmatter only → optionally convert legacy dataset outputs through explicit dry-run-first migration. Dataset migration is additive and never copies the underlying data into the wiki.

Archive

See references/archive.md. Flow: Move whole topic wikis from HUB/topics/<slug>/ to HUB/topics/.archive/<slug>/ → mark wikis.json with status: archived → hide them from normal query/compile/research/collect/output/maintenance context → restore by moving the folder back and setting status: active. Do not archive individual raw sources or compiled articles in v1.

Compilation

See references/compilation.md. Flow: Survey uncompiled sources → plan articles → classify (concept/topic/reference) → write/update articles with cross-references → update all indexes.

Query

Flow: Read _index.md → identify relevant articles by summary/tag → read articles → follow See Also links → Grep for additional matches → synthesize answer with citations → note gaps → peek active sibling wikis. Supports --resume to reload context after a session break — reads session files, recent log entries, wiki stats, and last-updated articles to produce a "where you left off" briefing. Deep queries may peek archived sibling indexes in a separate Archived Matches section; full archived reads require explicit user intent.

Linting

See references/linting.md. Flow: Check structure → indexes → links → content → coverage → report → optionally auto-fix. Default lint keeps active material healthy and reports archived topics as skipped. Use --include-archived or --archived-only for explicit archived structural maintenance.

Librarian

See references/librarian.md. Flow: Scan the active topic's compiled wiki/ layer → score staleness, quality, source-chain integrity, and link health → write .librarian/scan-results.json and .librarian/REPORT.md → recommend ranked next actions. Optional --passes conventions (or legacy schema) may write a proposal output for topic-guide improvements. Topic guides are default for new topic wikis; older wikis can adopt one with llm-wiki schema adopt or llm-wiki lint --fix. Librarian must not rewrite schema.md without explicit user acceptance. Librarian is the article-health advisor; it does not replace lint's structural checks or audit's broader trust review.

Audit

See references/audit.md. Flow: Run or reuse the librarian pass → inspect artifact dependency chains across output/, wiki/, and raw/ → escalate with fresh source checks and targeted research until trust verdicts converge → write .audit/REPORT.md.

Search

Flow: Scan indexes for summary/tag matches → Grep full-text → rank results → present.