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.
5. Which timezone should the wiki's timestamps use? → timezone: in index.md (not .env)
   • Optional. An IANA name such as America/Detroit; blank means UTC in the Z spelling.
   • Lives in the vault so it applies to every writer (CLI, server, Python API) and travels with it.
   • Written by obsidian-wiki setup --timezone <name> (step 3 below) or by hand; obsidian-wiki memory now prints stamps in it.
   • 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.
6. 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
7. 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

After resolving config, assign the global config directory with the exact obsidian_wiki_config_dir algorithm from the Config Resolution Protocol in skills/llm-wiki/SKILL.md. Create the shared writing profile only when it does not already exist. Preserve an existing $GLOBAL_CONFIG_DIR/WRITING.md; never overwrite it and do not ask additional writing-style questions.

Use OBSIDIAN_WIKI_REPO when it was loaded from config. When it is absent, derive the absolute repository/data root from this loaded skill's absolute path. Packaged installs and source checkouts both use <root>/skills/wiki-setup/SKILL.md; checkouts from before the rename used <root>/.skills/wiki-setup/SKILL.md. Then check both template layouts:

• Current: <root>/skills/llm-wiki/references/WRITING.md
• Older checkout: <root>/.skills/llm-wiki/references/WRITING.md

GLOBAL_CONFIG_DIR="$(obsidian_wiki_config_dir)"
mkdir -p "$GLOBAL_CONFIG_DIR"

SKILL_FILE="<absolute path of this loaded wiki-setup/SKILL.md>"
SKILL_DIR="$(cd "$(dirname "$SKILL_FILE")" && pwd)"
if [ -n "${OBSIDIAN_WIKI_REPO:-}" ]; then
  WIKI_ROOT="${OBSIDIAN_WIKI_REPO%/}"
else
  case "$SKILL_DIR" in
    */.skills/wiki-setup) WIKI_ROOT="${SKILL_DIR%/.skills/wiki-setup}" ;;
    */skills/wiki-setup) WIKI_ROOT="${SKILL_DIR%/skills/wiki-setup}" ;;
    *) echo "Cannot derive writing-profile template root from $SKILL_DIR" >&2; exit 1 ;;
  esac
fi

WRITING_TEMPLATE=""
for candidate in \
  "$WIKI_ROOT/skills/llm-wiki/references/WRITING.md" \
  "$WIKI_ROOT/.skills/llm-wiki/references/WRITING.md"
do
  if [ -f "$candidate" ]; then
    WRITING_TEMPLATE="$candidate"
    break
  fi
done
[ -n "$WRITING_TEMPLATE" ] || { echo "Writing profile template not found under $WIKI_ROOT" >&2; exit 1; }

WRITING_PROFILE="$GLOBAL_CONFIG_DIR/WRITING.md"
if [ ! -e "$WRITING_PROFILE" ]; then
  cp "$WRITING_TEMPLATE" "$WRITING_PROFILE"
fi

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 move the originals into _raw/_archived/ (created on first use).
• _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

obsidian-wiki setup --vault <path> [--timezone <IANA name>] creates all of these in one go. The templates below are what it writes, for setups done by hand.

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.*

.manifest.json

Create an empty manifest so ingest skills have a tracking file to append to and obsidian-wiki doctor reports the vault as complete (it treats .manifest.json as a required core file):

printf '{}\n' > "$OBSIDIAN_VAULT_PATH/.manifest.json"

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,
  "enabledCssSnippets": ["obsidian-wiki-folders"]
}

Folder colors and graph defaults

obsidian-wiki setup also writes .obsidian/snippets/obsidian-wiki-folders.css (one color per category folder in the file explorer, _ folders dimmed) and .obsidian/graph.json (the same colors in graph view, with _raw/, _archives/, _staging/, _meta/, index, log, and hot filtered out). If the CLI is available, run obsidian-wiki setup --vault "$OBSIDIAN_VAULT_PATH" rather than writing them by hand. Never overwrite an existing .obsidian file; to recolor later, use graph-colorize.

Step 5: Recommend Obsidian Plugins

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

1. Dataview — Query page metadata, create dynamic tables. Essential for a wiki.
2. Graph Analysis — Enhanced graph view for exploring connections.
3. Templater — If they want to create pages manually using templates.
4. 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
• index.md frontmatter carries timezone: if the user chose one (obsidian-wiki memory status shows the zone in use)
• log.md exists at vault root
• hot.md exists at vault root
• .manifest.json exists at vault root (empty {} is fine)
• .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)
• WRITING_PROFILE exists at the resolved global config directory
• Source directories (if configured) exist and are readable

Report the results, including the resolved absolute WRITING_PROFILE path, and tell the user they can now:

1. Open the vault in Obsidian (File → Open Vault → select the directory)
2. Run wiki-status to see what's available to ingest
3. Run wiki-ingest to add their first sources
4. Run claude-history-ingest to mine their Claude conversations
5. Run codex-history-ingest to mine their Codex sessions (if they use Codex)
6. Run wiki-status again anytime to check the delta

Optional: Install the Stop Hook (Auto-Capture)

Ask the user: "Want to auto-capture findings at session end?"

If yes, install the Stop hook into their global Claude Code settings so that every session with meaningful work automatically prompts /wiki-capture --quick before closing.

What the hook does: reads the session transcript on Stop, counts file edits and shell calls, and if significant work happened, asks Claude to run /wiki-capture --quick once. The wiki-capture quick-mode KEEP/SKIP gate prevents noise — routine or inconclusive sessions are skipped automatically.

Installation steps:

1. Find the obsidian-wiki repo path. If OBSIDIAN_WIKI_REPO is set in config, use that. Otherwise, check common locations: ~/Documents/projects/obsidian-wiki, ~/obsidian-wiki, or ask the user.

2. Locate the wiki-stop-capture.sh script. Its path differs between a pip/uv install and a source checkout, so check both layouts under <REPO_PATH> and use the first that exists:

   • <REPO_PATH>/hooks/wiki-stop-capture.sh — packaged install (OBSIDIAN_WIKI_REPO points at the bundled _data/ dir, which ships the hook under hooks/).
   • <REPO_PATH>/.claude/hooks/wiki-stop-capture.sh — source checkout.

   If neither exists (e.g. an older wheel that predates bundling the hook), fetch the canonical copy to a stable location and point at that instead. Use the global config dir from the Config Resolution Protocol in llm-wiki/SKILL.md (XDG-style ~/.config/obsidian-wiki by default, or the legacy ~/.obsidian-wiki if that already exists):

   CONFIG_DIR="$( [[ -d "$HOME/.obsidian-wiki" && ! -e "${XDG_CONFIG_HOME:-$HOME/.config}/obsidian-wiki" ]] && echo "$HOME/.obsidian-wiki" || echo "${XDG_CONFIG_HOME:-$HOME/.config}/obsidian-wiki" )"
   mkdir -p "$CONFIG_DIR/hooks"
   curl -fsSL https://raw.githubusercontent.com/Ar9av/obsidian-wiki/main/.claude/hooks/wiki-stop-capture.sh \
     -o "$CONFIG_DIR/hooks/wiki-stop-capture.sh"
   chmod +x "$CONFIG_DIR/hooks/wiki-stop-capture.sh"

   Use the resolved absolute path as <HOOK_PATH> below.

3. Merge the hook entry into ~/.claude/settings.json:

{
  "hooks": {
    "Stop": [
      {
        "matcher": "",
        "hooks": [
          {
            "type": "command",
            "command": "bash <HOOK_PATH>"
          }
        ]
      }
    ]
  }
}

If ~/.claude/settings.json already exists and has a hooks.Stop array, append the new entry rather than replacing — don't clobber existing hooks.

Note — expect a duplicate nudge inside this repo. The obsidian-wiki repo ships its own git-tracked .claude/settings.json registering the same Stop hook at a relative path. Claude Code merges project-level and user-level hook config rather than letting one override the other, so sessions ending inside the repo itself fire both registrations. This is expected and harmless — the hook claims an atomic per-session sentinel, so only one nudge is emitted. Leave both in place: removing the project entry dirties a tracked framework file and disables capture for anyone who clones the repo without doing the global install.

4. Confirm: "Stop hook installed. Claude Code will prompt /wiki-capture --quick at the end of any session where you write files or run ≥ 4 shell commands."

To uninstall later: remove the hook entry from ~/.claude/settings.json or set WIKI_STOP_CAPTURE=false in your shell to skip capture for a single session (HIVEMIND_CAPTURE=false is still honoured).

Optional: Configure GitHub Sync

Ask the user: "Want to sync your vault to a private GitHub repo?"

The vault is plain markdown, so pushing it to git gets you version history, backup, and cross-device sync for free. This is opt-in — skip it if the user declines or has no repo ready.

If yes:

1. Ask for the repo URL (e.g. https://github.com/you/my-wiki.git). Recommend it be private if the vault holds personal notes.
2. Run the CLI, which handles git init, a default .gitignore, and wiring the origin remote — this is the same code path obsidian-wiki setup's interactive prompt and setup.sh use, so there's one implementation to keep correct (see issue #153 for why that matters):

   obsidian-wiki sync-setup "<repo-url>" --vault "$OBSIDIAN_VAULT_PATH"

   If the obsidian-wiki binary isn't on PATH (source checkout without an install), run it from the repo instead: PYTHONPATH="$OBSIDIAN_WIKI_REPO" python3 -m obsidian_wiki.cli sync-setup ... using whichever of OBSIDIAN_WIKI_REPO or a local checkout path is available.
3. Tell the user they can run obsidian-wiki sync any time afterward to commit and push pending vault changes (stages everything, commits with a timestamp, pushes). There's no config file to check for sync status — the vault's own git remote is the source of truth.

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. Before running it, confirm the _raw/ exclusion described in Step 1.4 is in place — otherwise this update indexes the (currently empty) staging directory into the wiki collection too, and every future draft dropped there joins it silently.