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

• Optional. Enables semantic search in wiki-query and source discovery in wiki-ingest .

• If unsure, skip for now — both skills fall back to Grep automatically.

• Install instructions: see .env.example (QMD section).

Step 2: Create Vault Directory Structure

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

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

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

• .env has OBSIDIAN_VAULT_PATH set

• .obsidian/ directory exists

• 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