Your First Vault

A vault is the heart of Atlas. Understanding what it is — and what Atlas creates inside it — will help you get the most out of the app.

What Is a Vault?

A vault is just a folder on your computer. Atlas reads and writes plain markdown (.md) files inside it. There’s no proprietary database, no hidden format, and no lock-in.

This means:

• You can open any of your notes in any text editor
• You can back up your vault with a regular file backup or sync tool
• You can put your vault in a Git repository for version history
• You can sync it with Dropbox, iCloud, or any folder-syncing service

Note

Atlas never uploads your vault contents to the cloud. Your files stay on your machine.

Choosing a Vault Folder

When you launch Atlas for the first time, it asks you to choose a vault folder. You have two options:

Start fresh: Create a new, empty folder (e.g., My Atlas Vault in your Documents). Atlas will set everything up for you.

Use existing notes: Point Atlas at a folder that already contains markdown files. Atlas will index them without modifying your existing content, and will add its own atlas/ subfolder alongside your files.

Tip

If you’re already using Obsidian, Logseq, or another markdown app, you can point Atlas at the same folder. Atlas and those apps can share the same vault without conflicts.

What Atlas Creates

When you open a vault for the first time, Atlas creates a few folders to manage your data:

• DirectoryYourVault/

  • Directoryatlas/

    • Directoryidentity/

      • persona.md Atlas’s personality and communication style
      • user.md Your profile — name, role, preferences
      • intro.md First-run onboarding guide (deleted after completion)
    • Directorymemory/

      • Directorylong-term/

        • facts.md What Atlas has learned about you
      • Directorysessions/ Conversation transcripts (JSONL files)

        • …
      • Directoryfunctions/

        • schedule.md Scheduled automation tasks
        • drumbeat.md Ambient awareness configuration
        • quotes.md Dashboard quotes
    • Directoryrules/

      • rules.md How Atlas should behave
      • tools.md Tool usage guidance
      • allowed-tools.md Which tools are enabled (opt-out list)
    • Directorynetwork/

      • Directorypeople/ Your contacts

        • …
      • Directoryorganizations/ Companies and groups

        • …
      • Directorytopics/ Tags and topics in your network

        • …
    • Directorylogs/

      • actions-YYYY-MM.jsonl Agent action audit log
  • Directorydaily/

    • 2026-02-24.md Today’s daily note
  • your-existing-notes.md Your files, untouched

Note

All of these files are plain text. You can read and edit them directly. Be careful when editing files inside atlas/memory/ and atlas/rules/ — Atlas reads them closely and changes you make will affect its behavior.

Understanding the Key Files

atlas/identity/user.md

This is your profile. Atlas reads it to understand who you are. Over time, Atlas adds a ## Snapshot section that summarizes recent patterns in your conversations — your current projects, preferences, and context.

You can edit this file directly to tell Atlas things about yourself.

atlas/memory/long-term/facts.md

This is where Atlas stores things it learns about you: facts, goals, important relationships, and active projects. It’s organized into sections (## Facts, ## Goals, ## Relationships, ## Projects) and grows over time as you have more conversations.

atlas/rules/allowed-tools.md

This file controls which tools the Atlas agent can use. By default, all tools are enabled. To disable a tool, add a # before its name in this file.

daily/

Each day, Atlas creates a daily note (YYYY-MM-DD.md) in this folder. You can use it for journaling, tasks, or anything you want. Atlas can also write to it — adding tasks, notes from conversations, or a daily briefing.

Adding Your Own Notes

You don’t have to do anything special to add notes. Just put .md files in your vault folder (or any subfolder). Atlas will detect the new files and index them automatically.

After adding a batch of existing notes, you can trigger a manual re-index from Settings > Vault > Re-index Vault to make sure they’re all searchable right away.

Tip

Files in the atlas/ subfolder are intentionally excluded from regular vault search results — they’re internal to Atlas. Your own notes in the rest of the vault are fully searchable.

Switching Vaults

You can have multiple vaults and switch between them. Each vault is completely independent — separate notes, separate memory, separate settings.

To switch vaults: go to Settings > Vault > Change Vault Path and choose a different folder.

Atlas remembers your recently used vaults, so switching back is quick. Look for the vault selector at the bottom of the Settings panel.

Backing Up Your Vault

Since your vault is just a folder of text files, backing it up is simple:

• Manual backup: Copy the folder to an external drive or cloud storage
• Automated backup: Include it in your regular backup software
• Version control: git init in your vault folder for full history and diffs
• Cloud sync: Dropbox, iCloud Drive, Google Drive, or similar will sync it across your devices

Caution

If you sync your vault across devices using a cloud service, make sure Atlas is not running on two devices at the same time with the same vault. Simultaneous writes can cause file conflicts.