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A vault is the folder at the heart of every Second Brain session. Everything the agents read, create, and edit lives inside it.

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What is a vault?

An Obsidian vault is a plain folder of markdown files on your filesystem. Second Brain treats that folder as its workspace: when you open a vault, the app scans every file and builds a local index so the agents have complete context across all your notes — not just the ones you paste into the prompt. The index stores each note’s content, [[wikilinks]], #tags, and folder structure in a local SQLite database. Agents query this database to understand how your notes relate to each other before they plan or write anything.

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Types of vaults

Workspace vaults

Created inside Second Brain’s built-in obsidian-vaults/ directory. Use the Create New tab in the Vault Launcher to add one. These appear under the Recent Vaults tab automatically.

External vaults

Any folder already on your filesystem. Use the Browse Local tab in the Vault Launcher to select an existing Obsidian vault by path. The app adds it to your recent list once opened.

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Opening a vault

When you open or switch to a vault, Second Brain:
  1. Clears the previous index.
  2. Walks every file and folder in the vault directory (hidden folders starting with . are skipped).
  3. Reads the content of markdown, text, and other supported file types into the SQLite index.
  4. Extracts [[wikilinks]] and #tags from every .md file to build a relationship map.
After sync completes, the agents can read any note by path, follow links between notes, and understand the full folder hierarchy — without you having to copy and paste anything manually.

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Vault persistence

The path of the last active vault is saved to your .env file automatically. The next time you launch Second Brain, it reopens that vault and re-syncs it so the agents are always working with up-to-date content.

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Switching vaults

Click ↗ Switch vault in the sidebar at any time to return to the Vault Launcher. Selecting a different vault clears the current index and syncs the new one before you can send prompts.
Agents write directly to your vault files on disk. Before running any bulk operation — reorganizing folders, generating large numbers of notes, or deleting files — back up your vault. Copy the folder to a safe location or commit it to a Git repository so you can recover from unintended changes.