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. 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. 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.

Cross-Workflow Inventory Awareness

Inventory is first-class operational state, not a silo. Other workflows should notice it without treating it as factual evidence:

• Ingest and ingest-collection: if the user wants to track before ingesting, or a source is too large/ambiguous, suggest an inventory record. When an inventory candidate is ingested, link the resulting raw or collection manifest from the record.
• Dataset: link dataset manifests to inventory records when the user cares about next actions, priority, acceptance state, or why the corpus matters.
• Compile and query: use inventory to surface gaps, candidates, and next actions, but cite raw/wiki sources for factual claims.
• Collect: write the catalog as an output first, then create per-item inventory records only for small durable lists; use one corpus record for medium/large, unstable, or media-heavy collections.
• Research, audit, librarian, refresh, plan, and output: propose inventory records for durable follow-ups, stale items, source queues, or watch lists, but show a sample before creating a larger backlog.

Sessions

See references/sessions.md. Flow: Opt in with session enable → harness hooks append redacted events under HUB/.sessions/queue/ → session state and markdown digests update at tool-count, compaction, stop/session-end, or manual checkpoints → session rehydrate returns a compact context block → session promote explicitly copies the distilled digest into a topic raw/notes/ note. Automated capture is allowed; automated promotion is not.

Feedback Curator

See references/feedback.md. Flow: trusted user-prompt hooks or feedback capture classify high-signal user corrections, preferences, approvals, and plan-acceptance turns → append redacted candidates under HUB/.sessions/feedback/ → feedback list/show review them → feedback promote explicitly writes selected candidates into topic raw/notes/. Ignore generic acknowledgements unless manually captured.

Output

Flow: Gather relevant articles → generate artifact (summary/report/slides/etc) → save to output/ → update indexes.

Lessons Learned (ll)

Flow: Scan session for error→fix patterns, corrections, discoveries → extract structured lessons → write to raw/notes/ with type: lessons-learned → optionally update relevant articles → optionally suggest CLAUDE.md rules.

Links: File Paths and URLs

Terminal links break when they wrap to a second line. Rules for all wiki operations:

1. Full absolute paths — expand ~, HUB, and all relative segments. Relative paths are not clickable.
2. Markdown link syntax for URLs — use [short text](url), never bare long URLs that wrap and break.
3. No indentation before links — indentation eats terminal width. Put links flush-left on their own line.
4. One link per line — don't embed a long path mid-sentence. Break it out:

   Saved to:
   /Users/name/wiki/topics/my-topic/output/report-2026-04-08.md
   

See references/research-infrastructure.md § Agent Prompt Templates for examples. Applies to ingest, compile, collect, research, output, assess.

Activity Log

Every wiki operation appends to log.md in the wiki root. Format: ## [YYYY-MM-DD] operation | Description. See references/wiki-structure.md for full format. Never edit or delete existing log entries except during an explicit user-directed retraction with --remove-from-logs.

Confidence Scoring

Wiki articles include a confidence field in frontmatter: high, medium, or low.

• high: Multiple peer-reviewed sources agree, well-established knowledge
• medium: Single source, or sources partially agree, or recent findings not yet replicated
• low: Anecdotal, single non-peer-reviewed source, or sources disagree

When answering queries, note confidence levels. When linting, flag low confidence articles for review.

Compilation Nudge

Track uncompiled sources by comparing raw/_index.md ingestion dates against the last compile date in _index.md. If 5+ uncompiled sources exist after an ingestion, suggest: "You have N uncompiled sources. Run /wiki:compile to integrate them."

Structural Guardian

Automatically run a quick structural check when any of these triggers occur:

Triggers

• After any write operation (ingest, compile, collect, research, output, inventory, dataset, archive) — verify what was just written
• When the skill activates and the wiki hasn't been linted in 7+ days (check "Last lint" in _index.md)
• When content is found in the wrong place — articles in the global hub instead of a topic sub-wiki
• When a user mentions wiki problems — "wiki is broken", "empty", "missing", "wrong"
• When no wiki exists (first-run) — switch to guided onboarding flow instead of showing a command list. Walk the user through topic selection → init → first action suggestion. See commands/wiki.md § "If no wiki exists".

Quick Structure Check (lightweight, runs inline — not a full lint)

1. Hub integrity: The hub (HUB) should ONLY contain wikis.json, _index.md, log.md, topics/, and optional .sessions/ and .skills/. Validate .skills/ against the instruction-only package and active-topic allowlist contract. If raw/, wiki/, inventory/, datasets/, output/, inbox/, or config.md exist at the hub level → warn, do not delete. These may hold user data from an older wiki layout. Suggest /wiki:lint --fix, which will move contents to the appropriate topic wiki, repair archive registry drift, or quarantine to inbox/.unknown/ per C11/C12/C16/C17/C19 in references/linting.md.

2. Index freshness: For the active topic wiki, compare actual file counts in raw/, wiki/, inventory/, and datasets/ subdirectories against the rows in their _index.md. Ignore maintenance/report areas such as .librarian/ and .audit/. If mismatched → auto-fix by regenerating the affected directory index from frontmatter and removing dead entries.

3. Orphan detection: Check if any .md files exist in wiki directories but are not listed in any _index.md. If found → add them to the index.

4. Missing directories and legacy metadata: Verify core topic wiki subdirectories exist (raw/articles/, raw/papers/, wiki/concepts/, wiki/references/, output/, etc.). If missing → create them with empty _index.md. Treat inventory/ and datasets/ as lazy optional layers: repair their indexes if they already exist, but do not create completely absent optional trees unless the current inventory or dataset workflow needs them. For older compiled articles, lint --fix may infer category, summary, dates, and volatility from the file location and existing body/frontmatter, and may rewrite fuzzy raw-source refs to exact raw/...md paths when the match is unambiguous.

5. wikis.json sync: Check that all topic sub-wikis under HUB/topics/ are registered in wikis.json. Store hub-owned topic paths as portable relative paths (topics/<slug>), not /Users/<name>/... absolute paths. If a directory exists but isn't registered → add it. If a registered path is stale but HUB/topics/<name> exists → repair the path. If registered but no matching directory exists → remove the entry.

   Archived topic sub-wikis under HUB/topics/.archive/ should be registered with path: topics/.archive/<slug> and status: archived. Do not include them in active status/query/compile defaults.

6. Log existence: Verify log.md exists in the active wiki and at the hub. If missing → create it.

Behavior

• Silent when clean — don't report anything if everything checks out
• Auto-fix trivial issues — missing indexes, unregistered wikis, orphan files. Just fix and note in log.
• Warn on structural problems — content in wrong place, missing directories, stale indexes. Tell the user what's wrong and suggest /wiki:lint --fix.
• Never block the user's request — run the check, fix what you can, report issues, then continue with what the user actually asked for.

Concurrency

Multiple Claude Code sessions can safely read and write to the same wiki simultaneously. No locks are needed.

• Indexes are derived from the actual files on disk. If two sessions write articles at the same time, the next read rebuilds the index from whatever files exist. Both rebuilds converge to the same correct result.
• log.md is append-only with small atomic writes. Concurrent appends are safe. The explicit privacy-retraction exception rewrites the file atomically and should not run concurrently with other wiki writes.
• Article/source files are written independently. Two sessions creating different files never conflict. Two sessions editing the same file is unlikely and handled by last-write-wins (acceptable for a wiki — the content is always rebuildable from raw sources).

See references/indexing.md for the Derived Index Protocol.

Session Management

Research Session Registry

When a --min-time research or thesis session is active, the wiki root contains a .research-session.json or .thesis-session.json file.

Durable provenance should also live in the wiki root:

• .session-events.jsonl — append-only event log for replayable history
• .session-checkpoint.json — latest compact summary for resume briefings and audits

The session registry files are ephemeral crash-recovery state. The event log and checkpoint are the durable provenance trail.

Structural Guardian behavior:

• If a session file exists with status: "in_progress" and start_time > 7 days ago → warn: "Stale research session found. Clean up with /wiki:research or delete manually."
• Session files are ephemeral — never included in structural health checks or index counts
• Session files should NOT be committed to git
• .session-events.jsonl and .session-checkpoint.json should normally be preserved after completion so /wiki:audit can classify provenance as replayable instead of partial

Harness Session Capture

Automated Codex/Claude/OpenCode/Gemini session capture uses HUB/.sessions/ (or .wiki/.sessions/ for local wikis). This is a hidden operational layer for redacted hook events, state JSON, derived indexes, and markdown session digests. It is not topic evidence until explicitly promoted.

See references/sessions.md for the storage layout, config modes, hook adapter contract, rehydration behavior, and promotion rules.