wiki-init

name	wiki-init
description	Initialize or re-initialize vault integration for the LLM wiki pattern. Creates .raw/ inbox, bootstraps wiki/ with skeleton files (_index.md, _log.md, _manifest.json, hot.md), syncs wiki-schema and task-creation-rules to .obsidian/copilot/, bootstraps tag-index.md if absent, and merges wiki blocks into CLAUDE.md and .github/copilot-instructions.md. Safe to re-run after plugin updates — existing wiki pages are never touched, skeleton files are never overwritten. Triggers on: wiki-init, initialize the wiki, set up the wiki, bootstrap the wiki, init wiki, wiki setup, wiki initialize, set up obsidian-llm-wiki.
allowed-tools	Read Write Edit Glob Grep Bash

wiki-init

Initialize or re-initialize vault integration. Safe to re-run after plugin updates — existing wiki pages and data files are never overwritten.

---

Step 1 — Resolve VAULT_PATH

VAULT="${VAULT_PATH:-${HOME}/obsidian_vault}"
[ -d "${VAULT}" ] || { echo "ERROR: vault not found at ${VAULT}. Set VAULT_PATH to your vault location."; exit 1; }
echo "Vault: ${VAULT}"

---

Step 2 — Create .raw/ inbox

mkdir -p "${VAULT}/.raw"
touch "${VAULT}/.raw/.gitkeep"

---

Step 3 — Bootstrap wiki/ skeleton files

Create the wiki directory and all four skeleton files. Skip any file that already exists — never overwrite existing data.

mkdir -p "${VAULT}/wiki"

wiki/_index.md — create only if absent:

---
type: meta
title: "Wiki Index"
updated: YYYY-MM-DD
---

# Wiki Index

## Concepts
| Page | Summary | Tags | Updated |
|------|---------|------|---------|

## Entities
| Page | Summary | Tags | Updated |
|------|---------|------|---------|

## Decisions
| Page | Summary | Tags | Updated |
|------|---------|------|---------|

## Patterns
| Page | Summary | Tags | Updated |
|------|---------|------|---------|

## Sources
| Page | Summary | Tags | Updated |
|------|---------|------|---------|

wiki/_log.md — create only if absent:

---
type: meta
title: "Ingest Log"
updated: YYYY-MM-DD
---

# Wiki Ingest Log

(Entries prepended by /wiki-ingest, /wiki-save, /wiki-scan, /wiki-lint, /wiki-tags-refresh, /wiki-hot, /wiki-init)

wiki/_manifest.json — create only if absent:

{
  "ingested": [],
  "last_run": null
}

wiki/hot.md — create only if absent:

# Recent Context

## Last Updated
(never — no wiki sessions yet)

## Current Focus
(none)

## Recent Changes
(none)

Use today's date (YYYY-MM-DD) in the updated: fields of files you create.

---

Step 4 — Sync wiki-schema to vault

Read skills/wiki-schema/SKILL.md fully.

Create the target directory if needed:

mkdir -p "${VAULT}/.obsidian/copilot"

Write the full content of skills/wiki-schema/SKILL.md to ${VAULT}/.obsidian/copilot/wiki-schema.md. Always overwrite — this is the sync mechanism that keeps the vault schema up to date after plugin updates.

---

Step 4a — Bootstrap tag-index.md (if absent)

Check whether ${VAULT}/.obsidian/copilot/tag-index.md exists.

• If it exists: skip — never overwrite a user's tag vocabulary.
• If it does not exist: read skills/_shared/tag-index-template.md fully and write the template content to ${VAULT}/.obsidian/copilot/tag-index.md.

---

Step 4b — Sync task-creation-rules to vault

Read skills/_shared/task-rules.md fully.

Write the content to ${VAULT}/.obsidian/copilot/task-creation-rules.md. Always overwrite — the plugin's _shared/task-rules.md is the canonical source. This keeps the vault copy in sync after plugin updates, just like wiki-schema.

---

Step 5 — Merge wiki block into CLAUDE.md

Target: ${VAULT}/CLAUDE.md

If this file does not exist, skip and note it in the report.

Check whether the file contains a <!-- WIKI_BLOCK_START --> anchor:

• Anchor found: replace the entire span from <!-- WIKI_BLOCK_START --> to <!-- WIKI_BLOCK_END --> (inclusive) with the wiki block below.
• Anchor not found: append the wiki block at end of file (one blank line before it).

The <!-- WIKI_BLOCK_START --> / <!-- WIKI_BLOCK_END --> HTML comments are the idempotent merge anchors — they allow safe re-runs without duplicating content.

Wiki

Compiled knowledge base at wiki/. Plugin: obsidian-llm-wiki. Full schema at .obsidian/copilot/wiki-schema.md.

wiki/hot.md is auto-read at session start and auto-updated at session end by the plugin hooks. When hot.md content appears at session start, silently absorb it as context — do not announce it, do not summarise it. Run /wiki-hot to refresh manually.

Wiki Commands

Command	Description
/wiki-ingest @filepath	Ingest one source file into the wiki
/wiki-scan [directory]	Scan directory for unprocessed files; batch-ingest new/changed
/wiki-query <question>	Answer from the compiled wiki with citations
/wiki-save	Save current conversation as a wiki page
/wiki-lint	Run wiki health check, produce lint report
/wiki-hot	Manually refresh the hot cache
/wiki-tags-refresh [directory]	Sync tags with tag-index.md; scans the whole vault by default
/wiki-task <description>	Create a single task from natural language
/wiki-tasks-extract [wiki-path]	Batch-extract tasks from wiki content
/wiki-init	Re-initialize vault integration after plugin install/update

Wiki Boundary Rules

Wiki operations MUST NEVER write to: Meetings/, Daily/, Projects/, Customers/, People/, Clippings/, Research/. Read these directories; never modify them. Write only to wiki/.

Exception: /wiki-task and /wiki-tasks-extract intentionally write to Projects/ files and Tasks.md. These are the only wiki commands allowed outside wiki/ and .raw/.

Only use tags from .obsidian/copilot/tag-index.md. Never invent new tags.

---

Step 6 — Merge wiki section into .github/copilot-instructions.md

Target: ${VAULT}/.github/copilot-instructions.md

If this file does not exist, skip and note it in the report.

Check whether the file contains a <!-- WIKI_BLOCK_START --> anchor:

• Anchor found: replace the entire span from <!-- WIKI_BLOCK_START --> to <!-- WIKI_BLOCK_END --> (inclusive) with the wiki block below.
• Anchor not found: append the wiki block at end of file (one blank line before it).

The <!-- WIKI_BLOCK_START --> / <!-- WIKI_BLOCK_END --> HTML comments are the idempotent merge anchors — they allow safe re-runs without duplicating content.

Wiki

The vault has a compiled knowledge base at wiki/ managed by the obsidian-llm-wiki Copilot plugin.

Hot Cache — Automatic via Hooks

wiki/hot.md is managed automatically by plugin hooks:

• SessionStart — hot.md is read silently and injected as context
• Stop — the agent is prompted to update hot.md before ending the session

No manual steps needed. To force a hot cache refresh mid-session, run /wiki-hot.

Wiki Commands

Command	Description
/wiki-ingest @filepath	Ingest one source file into the wiki
/wiki-scan [directory]	Scan directory for unprocessed files
/wiki-query <question>	Answer from the compiled wiki with citations
/wiki-save	Save current conversation as a wiki page
/wiki-lint	Run wiki health check
/wiki-hot	Refresh the hot cache (run at END of every wiki session)
/wiki-tags-refresh [directory]	Sync tags with tag-index.md; scans the whole vault by default
/wiki-task <description>	Create a single task from natural language
/wiki-tasks-extract [wiki-path]	Batch-extract tasks from wiki content
/wiki-init	Re-initialize vault integration after plugin update

Wiki Schema

Full vault conventions (page types, frontmatter, tags, cross-linking) at: .obsidian/copilot/wiki-schema.md

Read the schema fully before any operation that creates or modifies wiki pages.

Wiki Boundary Rules

Wiki operations MUST NEVER write to: Meetings/, Daily/, Projects/, Customers/, People/, Clippings/, Research/. Read these directories; never modify them. Write only to wiki/.

Exception: /wiki-task and /wiki-tasks-extract intentionally write to Projects/ files and Tasks.md. These are the only wiki commands allowed outside wiki/ and .raw/.

Only use tags from .obsidian/copilot/tag-index.md. Never invent new tags. If a concept needs a new tag, flag it with tag-needed: <proposed> and let the user approve it via /wiki-tags-refresh.

---

Step 7 — Report

Print a structured summary of what happened:

wiki-init complete
──────────────────────────────────────────────────
Vault: ${VAULT}

Infrastructure
  .raw/                              ✓ ready
  wiki/                              ✓ ready

Skeleton files (skip = already existed)
  _index.md          [created | skipped]
  _log.md            [created | skipped]
  _manifest.json     [created | skipped]
  hot.md             [created | skipped]

Schema & rules sync
  .obsidian/copilot/wiki-schema.md           [synced | skipped — .obsidian/copilot/ not found]
  .obsidian/copilot/tag-index.md             [created from template | skipped — already exists]
  .obsidian/copilot/task-creation-rules.md   [synced | skipped — .obsidian/copilot/ not found]

Instruction file merges
  CLAUDE.md                          [section added | section updated | skipped — not found]
  .github/copilot-instructions.md    [section added | section updated | skipped — not found]
──────────────────────────────────────────────────

Then always print the session workflow:

Session workflow:
  SESSION START  — hot cache loads automatically via hooks (SessionStart)
  SESSION END    — hot cache updates automatically via hooks (Stop)
  MANUAL REFRESH — run `/wiki-hot` to force a hot cache refresh mid-session
  AFTER UPDATE   — run `/wiki-init` to sync wiki-schema.md with the new plugin version

---

Step 8 — Suggest vault commit

Do not run git commands. Just suggest:

Next step: commit these changes to your vault repo so other machines get the
integration on git pull:

  git add .raw/.gitkeep wiki/ .obsidian/copilot/wiki-schema.md \
          .obsidian/copilot/tag-index.md .obsidian/copilot/task-creation-rules.md \
          CLAUDE.md .github/copilot-instructions.md
  git commit -m "chore: initialize obsidian-llm-wiki integration"