AI Assistant Setup

AI Assistant Setup

Atlas can register its MCP server with Claude CLI, Claude Desktop, Codex, Cursor, Gemini, and GitHub Copilot. Client behavior and supported transport modes vary.

Automatic Setup

Preview all detected changes:

atlas bootstrap --dry-run

Apply them:

atlas bootstrap

Restrict setup to selected clients:

atlas bootstrap --only codex,claude,claude-desktop

Restart each assistant after changing its MCP configuration.

Repository-Pinned Setup

Use a repository-pinned local MCP configuration when one assistant should always query one index:

cd /path/to/repository
atlas index .

atlas install skill \
  --agent codex,claude,claude-desktop \
  --repo "$PWD" \
  --db "sqlite://$PWD/.atlas/atlas.db" \
  --server-url=none

Dynamic Workspace Setup

Bootstrap is appropriate when the assistant supplies the active workspace at runtime:

atlas bootstrap

Repository-scoped MCP tools still require one of:

• a workspace root supplied by the client
• a workspace argument
• a repository ID
• a repository pinned when MCP starts

If none is available, Atlas returns workspace_required instead of selecting a repository silently.

Shared Local Server

For multiple thin clients using one local service:

atlas serve --mcp --open=false

atlas install skill \
  --agent codex,claude,claude-desktop \
  --repo "$PWD" \
  --server-url http://127.0.0.1:3099

Use a token before exposing the service beyond loopback. See Dashboard and HTTP API.

Common Configuration Locations

Client	Typical location
Codex	~/.codex/config.toml
Claude CLI	~/.claude.json
Claude Desktop on macOS	~/Library/Application Support/Claude/

The Claude Desktop configuration filename is claude_desktop_config.json.

Atlas preserves unrelated client configuration. Always review a dry run before applying changes in managed environments.

Verify

atlas doctor --verify atlas
atlas status
atlas bootstrap --dry-run

Then ask the assistant a repository-specific question and confirm that the answer includes source file and line references.

Remove Integration

Preview removal:

atlas uninstall --dry-run

Apply removal:

atlas uninstall

This removes Atlas-managed assistant entries and skills. It does not remove unrelated assistant configuration or repository indexes.