LLM Wiki Manager

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.

Resolution order:

1. --local flag → .wiki/ in current project
2. --wiki <name> flag → named wiki from HUB/wikis.json
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. Once ingested into raw/, sources are never modified. They are a record of what was ingested and when. All synthesis happens in wiki/.

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.

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

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.

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 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.

Linting

See references/linting.md. Flow: Check structure → indexes → links → content → coverage → report → optionally auto-fix.

Search

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

Output

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

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, 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 — append only.

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, research, output) — 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, and topics/. If raw/, wiki/, 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 or quarantine to inbox/.unknown/ per C11/C12 in references/linting.md.

2. Index freshness: For the active topic wiki, compare actual file count in wiki/concepts/, wiki/topics/, wiki/references/ against the rows in their _index.md. If mismatched → auto-fix by adding missing entries or removing dead ones.

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: Verify all expected subdirectories exist in the topic wiki (raw/articles/, raw/papers/, etc.). If missing → create them with empty _index.md.

5. wikis.json sync: Check that all topic sub-wikis under HUB/topics/ are registered in wikis.json. If a directory exists but isn't registered → add it. If registered but directory is missing → remove the entry.

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.
• 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.

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