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-ingestwill 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
## Journallog.md
---
title: Wiki Log
---
# Wiki Log
- [TIMESTAMP] INIT vault_path="OBSIDIAN_VAULT_PATH" categories=concepts,entities,skills,references,synthesis,journalhot.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.mdexists at vault rootlog.mdexists at vault roothot.mdexists at vault root.envhasOBSIDIAN_VAULT_PATHset.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-statusto see what's available to ingest - Run
wiki-ingestto add their first sources - Run
claude-history-ingestto mine their Claude conversations - Run
codex-history-ingestto mine their Codex sessions (if they use Codex) - Run
wiki-statusagain anytime to check the delta