brain-index

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name: brain-index description: Indexes the local Obsidian vault at ~/Desktop/Obsidian/Brain/ into a local ChromaDB collection so /cto, /prd, /architect, and github-scout can do semantic retrieval (not keyword grep) against the owner's accumulated knowledge. Embeddings are computed locally via the default all-MiniLM-L6-v2 model — vault contents never leave the machine. Incremental: only re-embeds chunks whose content changed. Run on demand or via the nightly Stop-hook. triggers:

• /brain-index
• /brain-query args: "[index | query ""] [--top N] [--reset] [--vault PATH] [--collection brain|refs] [--domain frontend|backend|data|infra|product|content] [--surface identity|people|decisions|meetings|daily|projects|playbook|wiki|raw]"

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brain-index

You are operating the local brain index. The Obsidian vault is the owner's accumulated knowledge — opinions, decisions, meeting notes, project history, taste. The brain-index makes it semantically queryable so the orchestrator can pull relevant context on every run, not just files matching a keyword.

The data plane is a local ChromaDB at ~/.claude/brain-index/data/. The compute plane is a local venv at ~/.claude/brain-index/venv/. Nothing leaves the machine.

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Phase 0 — Setup (idempotent)

bash .claude/skills/brain-index/setup.sh

This creates the venv on first run (~200MB download) and is a no-op afterward.

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Phase 1 — Pick the operation

Two operations: index (refresh the vector DB from vault) and query (semantic retrieval).

Per-agent memory slice

Each chunk written by index.py carries two metadata fields the query side filters on:

• surface — top-level vault folder. Maps to identity / people / decisions / meetings / daily / projects / playbook / wiki / raw. Use --surface decisions to retrieve only from the Decisions/ folder.
• domains — comma-separated set inferred from heading + body keywords. Values: frontend / backend / data / infra / product / content. Use --domain backend to retrieve only chunks that mention backend keywords.

Filters stack via $and. Example: --domain backend --surface wiki returns wiki chunks tagged backend.

This is what /cto Phase 5 uses to give each engineering subagent its own slice of memory — backend agent sees backend context, frontend agent sees frontend context. Avoids cross-domain noise.

Index

source ~/.claude/brain-index/venv/bin/activate
python .claude/skills/brain-index/index.py

Default vault: ~/Desktop/Obsidian/Brain/. Override with --vault /custom/path. Default collection: brain. Use --reset to drop and rebuild the collection (rare; only after a major vault reorg).

Incremental indexing: chunks are keyed by sha256 of their text, so re-running only re-embeds what changed. A 1000-note vault refreshes in ~5 seconds after the first build.

Query

source ~/.claude/brain-index/venv/bin/activate
python .claude/skills/brain-index/query.py "<query text>" --top 10

Flags:

• --collection brain (default) or --collection refs (curated GitHub references)
• --top N — number of results (default 10)
• --json — JSON output instead of markdown

Markdown output is designed to drop directly into context for /cto Phase 1.

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Phase 2 — Wire into /cto

/cto Phase 1 (context load) calls this for semantic retrieval before generating any artifact:

# Inside /cto context-load phase
QUERY="<keywords + concepts from brief>"
python .claude/skills/brain-index/query.py "$QUERY" --top 8 --collection brain > outputs/<slug>/context-brain.md
python .claude/skills/brain-index/query.py "$QUERY" --top 5 --collection refs  > outputs/<slug>/context-refs.md

Both files are appended to the context bundle that /prd, /architect, and /createplan read.

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Phase 3 — Auto-refresh

Two patterns for keeping the index current:

Pattern A — Stop hook (recommended): add to .claude/settings.json so the index refreshes when the session ends:

{
  "hooks": {
    "Stop": [
      { "type": "shell", "command": "bash ~/.claude/brain-index/refresh.sh >/dev/null 2>&1 &" }
    ]
  }
}

(Backgrounded so it never blocks the prompt return.)

Pattern B — LaunchAgent / cron (overnight): run python index.py nightly at 3am. See ~/.claude/brain-index/launchd/ if you want the plist scaffolding.

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What gets indexed

• Every *.md and *.markdown file under ~/Desktop/Obsidian/Brain/
• Skipped: .obsidian/, .git/, .trash/, node_modules/, __pycache__/, hidden dirs
• Chunks: split by H2 headings; sliding window for sections >1200 chars

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What does NOT get indexed

• Anything outside the vault root
• PDFs, images, audio (chunk model is text-only)
• Files >80KB (rarely high-signal)

If you want PDF/audio coverage, that's a future skill — the embedding model would change.

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Privacy posture

• All data is local. The chromadb default model is all-MiniLM-L6-v2 (~80MB, runs on CPU).
• No API calls. No telemetry. Zero network during embed or query.
• Verify by running the indexer offline (turn off wifi after first install).

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Handoff

Indexed. N files, M chunks. Run /brain-query "<text>" to test, or /cto will auto-pull relevant context on its next run.