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:

-

Where should the vault live? → OBSIDIAN_VAULT_PATH

• Default: ~/Documents/obsidian-wiki-vault

• Must be an absolute path (after expansion)

-

Where are your source documents? → OBSIDIAN_SOURCES_DIR

• Can be multiple paths, comma-separated

• Default: ~/Documents

-

Want to import Claude history? → CLAUDE_HISTORY_PATH

• Default: auto-discovers from ~/.claude

• Set explicitly if Claude data is elsewhere

-

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).

-

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

-

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

mkdir -p "$OBSIDIAN_VAULT_PATH"/{concepts,entities,skills,references,synthesis,journal,projects,_archives,_raw,_staging,.obsidian}

• .obsidian/ — Obsidian's own config. Creates vault recognition.

• projects/ — Per-project knowledge (populated during ingest).

• _archives/ — Stores wiki snapshots for rebuild/restore operations.

• _raw/ — Staging area for unprocessed drafts. Drop rough notes here; wiki-ingest will promote them to proper wiki pages and delete the originals.

• _staging/ — Review queue for LLM-written pages when WIKI_STAGED_WRITES=true. Pages here are not visible in Obsidian's graph until promoted via /wiki-stage-commit.

Step 3: Create Special Files

index.md

---

title: Wiki Index

---

# Wiki Index

*This index is automatically maintained. Last updated: TIMESTAMP*

## Concepts

*No pages yet. Use `wiki-ingest` to add your first source.*

## Entities

## Skills

## References

## Synthesis

## Journal

log.md

---

title: Wiki Log

---

# Wiki Log

- [TIMESTAMP] INIT vault_path="OBSIDIAN_VAULT_PATH" categories=concepts,entities,skills,references,synthesis,journal

hot.md

---

title: Hot Cache

updated: TIMESTAMP

---

# Hot Cache

*A ~500-word semantic snapshot of recent activity. Updated after every major write operation.*

## Recent Activity

- [TIMESTAMP] INIT — vault created at OBSIDIAN_VAULT_PATH

## Active Threads

*None yet — start ingesting sources to populate.*

## Key Takeaways

*None yet.*

## Flagged Contradictions

*None yet.*

Step 4: Create .obsidian Configuration

Create minimal Obsidian config for a good out-of-box experience:

.obsidian/app.json

{

  "strictLineBreaks": false,

  "showFrontmatter": false,

  "defaultViewMode": "preview",

  "livePreview": true

}

.obsidian/appearance.json

{

  "baseFontSize": 16

}

Step 5: Recommend Obsidian Plugins

Tell the user about these recommended community plugins (they install manually):

• Dataview — Query page metadata, create dynamic tables. Essential for a wiki.

• Graph Analysis — Enhanced graph view for exploring connections.

• Templater — If they want to create pages manually using templates.

• Obsidian Git — Auto-backup the vault to a git repo.

Step 6: Verify Setup

Run a quick sanity check:

• Vault directory exists with: concepts/, entities/, skills/, references/, synthesis/, journal/, projects/, _archives/, _raw/

• index.md exists at vault root

• log.md exists at vault root

• hot.md exists at vault root

• .env has OBSIDIAN_VAULT_PATH set

• .obsidian/ directory exists

• _staging/ directory exists (required even when WIKI_STAGED_WRITES is not set — created on setup for future use)

• Source directories (if configured) exist and are readable

Report the results and tell the user they can now:

• Open the vault in Obsidian (File → Open Vault → select the directory)

• Run wiki-status to see what's available to ingest

• Run wiki-ingest to add their first sources

• Run claude-history-ingest to mine their Claude conversations

• Run codex-history-ingest to mine their Codex sessions (if they use Codex)

• Run wiki-status again anytime to check the delta

Optional: Refresh QMD After Setup

If QMD_WIKI_COLLECTION is configured and the local QMD CLI is available, run qmd update after the initial vault files exist so the fresh vault is immediately queryable. No embedding pass is usually needed at setup time because the vault starts empty, so a plain update is enough unless you have already populated pages.