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