wiki-setup

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---
name: wiki-setup
description: >
  Initialize a new Obsidian wiki vault with the correct structure, special files, and configuration.
  Use this skill when the user wants to set up a new wiki from scratch, initialize the vault structure,
  create the .env file, or says things like "set up my wiki", "initialize obsidian", "create a new vault",
  "get started with the wiki". Also use when the user needs to reconfigure their existing vault or
  fix a broken setup.
---

# Obsidian Setup — Vault Initialization

You are setting up a new Obsidian wiki vault (or repairing an existing one).

## Step 1: Create .env

If `.env` doesn't exist, create it from `.env.example`. Ask the user for:

1. **Where should the vault live?** → `OBSIDIAN_VAULT_PATH`
   - Default: `~/Documents/obsidian-wiki-vault`
   - Must be an absolute path (after expansion)

2. **Where are your source documents?** → `OBSIDIAN_SOURCES_DIR`
   - Can be multiple paths, comma-separated
   - Default: `~/Documents`
   - Local git repo clones (public or private, any host) can be listed here too — clone
     the repo locally first, then add its path. See "Ingesting Git Repositories" in
     `wiki-ingest/SKILL.md` for how repo sources are handled.

3. **Want to import Claude history?** → `CLAUDE_HISTORY_PATH`
   - Default: auto-discovers from `~/.claude`
   - Set explicitly if Claude data is elsewhere

4. **Have QMD installed?** → `QMD_WIKI_COLLECTION` / `QMD_PAPERS_COLLECTION` / `QMD_TRANSPORT`
   - Optional. Enables semantic search in `wiki-query` and source discovery in `wiki-ingest`.
   - Default to `QMD_TRANSPORT=mcp` unless the user wants the agent to call the local `qmd` CLI directly.
   - If using CLI mode, set `QMD_CLI_SEARCH_MODE=quality` by default; suggest `balanced` if reranking is too slow.
   - If unsure, skip for now — both skills fall back to `Grep` automatically.
   - Install instructions: see `.env.example` (QMD section).
   - **If `QMD_WIKI_COLLECTION` is set, verify the collection excludes `_raw/`.** The wiki
     collection and papers collection must stay disjoint — `wiki-query` cites them as
     separate layers (compiled knowledge vs. raw staging), and `OBSIDIAN_VAULT_PATH` contains
     `_raw/`, so a plain `qmd collection add <vault>` silently merges the two.
     Read `~/.config/qmd/index.yml`, find the entry for `$QMD_WIKI_COLLECTION`, and check its
     `ignore` list includes `_raw/**` (and ideally `log.md`, which has no semantic value). If
     the collection doesn't exist yet, create it (`qmd collection add "$OBSIDIAN_VAULT_PATH"
     --name <collection-name>`), then add the `ignore` block to `index.yml` by hand — `qmd`
     has no `--ignore` flag and refuses a second `collection add` on a path that already has
     one, so editing the YAML is the only way to scope it. Run `qmd update` after editing.
     If the collection already exists without the `ignore` block, tell the user their
     wiki collection is indexing `_raw/` (including `_raw/_archived/` drafts left behind by
     `wiki-ingest`) and offer to add the `ignore` block and re-run `qmd update`.

5. **Token budget warning threshold?** → `WIKI_TOKEN_WARN_THRESHOLD`
   - Default: `100000` (warn when full-wiki read would cost > 100K tokens)
   - Set to `0` to disable the warning entirely
   - `wiki-status` shows a token footprint table and emits this warning automatically

6. **Enable staged writes?** → `WIKI_STAGED_WRITES`
   - Default: unset / `false` (pages written directly to their final location)
   - Set to `true` for team wikis, high-stakes domains, or any vault where the human wants final say on every LLM-written page
   - When enabled: all new/updated pages land in `_staging/` first; run `/wiki-stage-commit` to review and promote them
   - `wiki-status` shows a "Staged writes pending" count when files are waiting

## Step 2: Create Vault Directory Structure

```bash
mkdir -p "$OBSIDIAN_VAULT_PATH"/{concepts,entities,skills,references,synthesis,journal,projects,_archives,_raw,_sta