wiki

# 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](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](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](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 + 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.

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.

## 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 thei