Set up agents and Deepnote Cloud access in VS Code and Cursor

[jamesbhobbs]

Deepnote's cloud features should work the same for any agent. That means VS Code with Copilot agent mode, Cursor's agent, and Claude Code or Codex in the integrated terminal. This issue sets up the pieces they all need; the buttons are tracked separately.

Current state

• The bundled CLI (dist/deepnoteCli.cjs, built from @deepnote/cli@0.8.0) is only used to run install-skills (src/kernels/deepnote/deepnoteAgentSkillsManager.node.ts). It isn't on PATH, so when the skill tells an agent to run deepnote …, the command fails.
• 0.8.0 has no publish.
• No MCP server is registered. The extension only uses vscode.lm.registerTool (src/standalone/chat/extension.node.ts), and Cursor ignores those tools.
• The extension has no way to store or read a Deepnote API token.
• Skills are installed only when a kernel starts, and only into workspaceFolders[0].
• configure_python_notebook and configure_non_python_notebook are registered in code but missing from contributes.languageModelTools.

Tasks

Token (.env file)

• "Deepnote: Set API Token":
  1. Check the token against the API.
  2. Write or update DEEPNOTE_TOKEN= in .env at the workspace or sync root.
  3. Make sure .env is in .gitignore, asking before editing that file.
• "Deepnote: Clear API Token" removes that line.
• Read the same .env to know whether the user is signed in. Features that need a token prompt for one when it's missing.
• Nothing is injected into terminals; the CLI and MCP server read .env themselves (Get deepnote sync and publish ready for the editor and agents deepnote#543, Add sync, publish and app tools to the local MCP server deepnote#544).

CLI

• Update the bundled CLI to the release from Get deepnote sync and publish ready for the editor and agents deepnote#543.
• Put deepnote on PATH for integrated terminals, without saving it to disk. Use a launcher in global storage that runs dist/deepnoteCli.cjs with ELECTRON_RUN_AS_NODE=1, added via environmentVariableCollection. Check that Cursor's agent terminal picks it up.

MCP

• Bundle @deepnote/mcp the same way the CLI is bundled.
• Register it in VS Code through mcpServerDefinitionProviders / vscode.lm.registerMcpServerDefinitionProvider. That needs VS Code 1.101+, and the engine is currently ^1.95, so turn it on only where it's supported.
• Register it in Cursor through Cursor's own API for registering MCP servers from an extension. If that isn't available, ask before writing .cursor/mcp.json.
• Use the existing interpreter sidecar (deepnote.json) and the .env token.

Skills and agent tools

• Install skills when the extension starts, for every workspace folder, and again after the extension updates.
• The skill should say that deepnote is on PATH, that MCP tools are available, and that the token lives in .env. Agents must never ask for the token or print it.
• Declare the two missing language model tools in package.json.

Done when

In each environment below, an agent can run deepnote sync --dry-run -o json or call deepnote_sync successfully in a fresh workspace, after only "Set API Token" (manual check):

• VS Code with Copilot agent mode
• Cursor agent
• Claude Code in the integrated terminal
• Codex in the integrated terminal

Blocked by deepnote/deepnote#543 and deepnote/deepnote#544. Related to #318.

🤖 Generated with Claude Code