The workspace is the agent's home: the working directory used for file tools and workspace context. Keep it private and treat it as memory.

This is separate from ~/.apus/, which stores config, credentials, and sessions.

The workspace is the default cwd, not a hard sandbox. Tools resolve relative paths against the workspace, but absolute paths can still reach elsewhere on the host unless sandboxing is enabled. If you need isolation, use agents.defaults.sandbox (and/or per-agent sandbox config).

When sandboxing is enabled and workspaceAccess is not "rw", tools operate inside a sandbox workspace under ~/.apus/sandboxes, not your host workspace.

Default location

Override in ~/.apus/apus.json:

{
  agents: {
    defaults: {
      workspace: "~/.apus/workspace",
    },
  },
}

Per-agent override: agents.entries.*.workspace. To keep main at an existing shared root in a multi-agent roster, pin agents.entries.main.workspace to that root explicitly; changing agents.defaults.workspace alone sets the base for unpinned entries.

Run workspace selection rejects an explicitly supplied blank or invalid agent ID. Omit the selector to use configured ownership, or supply the intended agent ID.

apus onboard, apus configure, or apus setup create the workspace and seed the bootstrap files if they are missing.

Sandbox seed copies only accept regular in-workspace files; symlink/hardlink aliases that resolve outside the source workspace are ignored.

If you already manage the workspace files yourself, disable bootstrap file creation:

{ agents: { defaults: { skipBootstrap: true } } }

Extra workspace folders

Older installs may have created ~/apus. Each agent uses one resolved workspace; keeping extra directories does not merge their persona or memory files into the active workspace.

Keep each agent's workspace path explicit when retaining older directories. Before switching back to an older workspace, stop the Gateway, configure the intended path, run apus doctor --fix to migrate retired setup state, and restart. Doctor also discovers legacy setup files in a still-configured agents.defaults.workspace root even when no agent currently uses that root directly. Archive unused folders only after verifying which files you want to retain.

Workspace file map

Use Settings → Agents → Files in the Control UI to edit these files. Preview shows the current draft; Edit returns to the editor so you can continue typing, while Close returns to Preview.

Standard files Apus expects inside the workspace:

AGENTS.md - operating instructions 
Operating instructions for the agent and how it should use memory. Loaded at the start of every session. Good place for rules, priorities, and "how to behave" details. Template: [AGENTS.md](/reference/templates/AGENTS).
SOUL.md - persona and tone 
Persona, tone, and boundaries. Loaded every session. Guide: [SOUL.md personality guide](/concepts/soul).
USER.md - directive-based user model (optional) 
Stable preferences, communication style, relationships, and active-project context. Write entries as dated active or superseded directives. Loaded every session with a separate 4,000-character budget. See [User model](/concepts/user-model). Template: [USER.md](/reference/templates/USER).
IDENTITY.md - name, vibe, emoji 
The agent's name, vibe, and emoji. Created/updated during the bootstrap ritual. Template: [IDENTITY.md](/reference/templates/IDENTITY).
AGENTS.md Tools section - local tool conventions 
The `## Tools` section holds local environment notes and conventions. It does not control tool availability; it is only guidance. Template: [AGENTS.md Tools section](/reference/templates/AGENTS#tools).
BOOT.md - startup checklist 
Optional startup checklist run on Gateway startup when the [boot-md hook](/automation/hooks/bundled-hooks#boot-md) is enabled. Enabling a different internal hook does not enable `boot-md`. Keep it short; use the message tool for outbound sends. Template: [BOOT.md](/reference/templates/BOOT).
BOOTSTRAP.md - first-run ritual 
One-time first-run ritual. Only created for a brand-new workspace. Delete it after the ritual is complete. Template: [BOOTSTRAP.md](/reference/templates/BOOTSTRAP).
memory/YYYY-MM-DD.md - daily memory log 
Daily memory log (one file per day). Recommended to read today + yesterday on session start.
MEMORY.md - curated long-term memory (optional) 
Curated long-term memory: durable non-profile facts, decisions, and short summaries. Keep detailed logs in `memory/YYYY-MM-DD.md` so memory tools can retrieve them on demand without injecting them into every prompt. Only load `MEMORY.md` in the main, private session (not shared/group contexts). See [Memory](/concepts/memory) for the workflow and automatic memory flush.
skills/ - workspace skills (optional) 
Workspace-specific skills. Highest-precedence skill location for that workspace, ahead of project agent skills, personal agent skills, managed skills, bundled skills, and `skills.load.extraDirs` when names collide.

If a required bootstrap file is missing, Apus injects a "missing file" marker into the session and continues. Optional USER.md and MEMORY.md files are omitted when absent. Large bootstrap files are truncated when injected; adjust general limits with agents.defaults.bootstrapMaxChars (default: 20000) and agents.defaults.bootstrapTotalMaxChars (default: 60000). USER.md keeps its separate 4,000-character cap. apus setup can recreate missing defaults without overwriting existing files.

The workspace document editor and agents.files.set accept up to 2 MiB of UTF-8 text per file. Larger saves are rejected before replacing the existing document. This byte limit is separate from prompt truncation settings and the identity form's avatar support.

What is NOT in the workspace

These live under ~/.apus/ and should NOT be committed to the workspace repo:

If you need to migrate sessions or config, copy them separately and keep them out of version control.

Older Apus releases wrote apus-workspace-state.json and .attested workspace sidecars. Current runtime uses only the shared SQLite database for that state. If Doctor reports one of these files, run apus doctor --fix; Doctor imports valid legacy state and deletes a source only after verifying the database rows. Empty reserved hashed files under workspace-attestations/ are discarded because they contain no importable state; other unreadable sources stay in place and Doctor names their paths.

The pre-July .apus/workspace-state.json layout is outside the supported migration window. Upgrade through 2026.9.7 and run apus doctor --fix there before updating; current Doctor leaves that file untouched. See the retention policy.

Git backup (recommended, private)

Treat the workspace as private memory. Put it in a private git repo so it is backed up and recoverable.

Run these steps on the machine where the Gateway runs (that is where the workspace lives).

Initialize the repo

If git is installed, brand-new workspaces are initialized automatically. If this workspace is not already a repo, run:

```bash
cd ~/.apus/workspace
git init
git add AGENTS.md SOUL.md IDENTITY.md USER.md memory/
git commit -m "Add agent workspace"
```

Add a private remote

GitHub web UI

    1. Create a new **private** repository on GitHub.
    2. Do not initialize with a README (avoids merge conflicts).
    3. Copy the HTTPS remote URL.
    4. Add the remote and push:

    ```bash
    git branch -M main
    git remote add origin <https-url>
    git push -u origin main
    ```

GitHub CLI (gh)

    ```bash
    gh auth login
    gh repo create apus-workspace --private --source . --remote origin --push
    ```

GitLab web UI

    1. Create a new **private** repository on GitLab.
    2. Do not initialize with a README (avoids merge conflicts).
    3. Copy the HTTPS remote URL.
    4. Add the remote and push:

    ```bash
    git branch -M main
    git remote add origin <https-url>
    git push -u origin main
    ```

Ongoing updates

```bash
git status
git add .
git commit -m "Update memory"
git push
```

Do not commit secrets

Even in a private repo, avoid storing secrets in the workspace:

  • API keys, OAuth tokens, passwords, or private credentials.
  • Anything under ~/.apus/.
  • Raw dumps of chats or sensitive attachments.

If you must store sensitive references, use placeholders and keep the real secret elsewhere (password manager, environment variables, or ~/.apus/).

Suggested .gitignore starter:

.DS_Store
.env
**/*.key
**/*.pem
**/secrets*

Moving the workspace to a new machine

Clone the repo

Clone the repo to the desired path (default `~/.apus/workspace`).

Update config

Set `agents.entries.<agentId>.workspace` to the cloned path in `~/.apus/apus.json` for the agent that should use it. A sole agent without a per-agent override can use `agents.defaults.workspace` instead; in a multi-agent roster, that setting only changes the base directory for unpinned entries.

Verify the workspace

Run `apus agents list` and confirm that the intended agent points to the cloned path before starting the Gateway. Moving an existing workspace does not require rerunning onboarding.

Copy sessions (optional)

If you need sessions, copy `~/.apus/agents/<agentId>/agent/apus-agent.sqlite`
from the old machine separately. Copy `~/.apus/agents/<agentId>/sessions/`
only when you also need legacy migration inputs or archive/support artifacts.

Advanced notes

Related