# Jessepinkman9900 Claude Second Brain Claude Second Brain

> Brain Refresh

- Skill: `tomevault-io/jessepinkman9900-claude-second-brain-claude-second-brain` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds@latest add tomevault-io/jessepinkman9900-claude-second-brain-claude-second-brain`
- Raw SKILL.md: https://api.skillmd.com/api/skills/tomevault-io/jessepinkman9900-claude-second-brain-claude-second-brain/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: tomevault-io (https://skillmd.com/u/tomevault-io)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/tomevault-io/jessepinkman9900-claude-second-brain-claude-second-brain

---


# Brain Refresh

Refreshes the qmd index so search reflects the current state of the vault. Wraps `pnpm qmd:reindex` (incremental) and the qmd CLI's force-embed flag.

## Brain Discovery

All commands target the **default brain** registered in `~/.claude-second-brain/config.toml`.
Resolve the brain root via the CLI and run qmd through the CLI proxy:

```bash
BRAIN_PATH=$(npx -y claude-second-brain path)
npx -y claude-second-brain qmd -- status
```

Pass `--brain <name>` before the `--` to target a non-default brain.

## When to Use

- After a `/brain-ingest` session (or several) — batch the refresh, don't run after every file edit
- After manual edits to `wiki/` or `raw-sources/` files
- When `/brain-search` results feel stale or miss recently added content
- After upgrading `@tobilu/qmd` or changing the embedding model — use `force` mode

## Procedure

All `pnpm qmd:*` commands must run from `$BRAIN_PATH`; the CLI proxy (`claude-second-brain qmd`) works from anywhere.

### Default — Incremental Refresh

Run:
```bash
cd "$BRAIN_PATH" && pnpm qmd:reindex
```

This script does two things:
1. **Update** — scans collections for new, changed, or deleted files and updates the index
2. **Embed** — generates vector embeddings for any chunks that need them

Only chunks that changed get re-embedded, so this is fast on subsequent runs.

### Force Mode (`force` argument)

When the user passes `force`, re-embed **every** chunk — not just the changed ones. Use after embedding-model changes or if embeddings appear corrupted.

```bash
# Step 1 — update the file index first
cd "$BRAIN_PATH" && pnpm qmd:reindex

# Step 2 — force re-embed everything
npx -y claude-second-brain qmd -- embed -f
```

Force mode is slow — confirm with the user before proceeding if the wiki is large.

## Verify

After refresh, confirm with:

```bash
npx -y claude-second-brain qmd -- status
```

Document and embedding counts should be non-zero and reflect recent activity. If embeddings show as `0` or far below document count, re-run the refresh.

## Notes

- First run downloads ~2GB of GGUF models — expected, one-time
- Do not run this after every single file edit — batch it after a session
- This skill does **not** change the qmd schema (collections, contexts). For that, use `/brain-rebuild`
- If `query` or `search` commands fail with "collection not found", run `pnpm qmd:setup` from the vault root to re-register collections, then re-run this skill

---
> Source: [jessepinkman9900/claude-second-brain](https://github.com/jessepinkman9900/claude-second-brain) — distributed by [TomeVault](https://tomevault.io).
<!-- tomevault:4.0:skill_md:2026-06-22 -->