Get deepnote sync and publish ready for the editor and agents #543

The VS Code / Cursor extension (deepnote/vscode-deepnote) and coding agents are going to drive deepnote sync and deepnote publish. Today they can't do that reliably. This issue collects the CLI changes they need.

Current state

• @deepnote/cli@0.8.0 on npm has no publish or static-site access; they exist only on main. deepnote streamlit publish is still in feat(cli): add deepnote streamlit publish #466.
• publish and static-site access output only human-readable text. -q hides the URL (packages/cli/src/commands/publish.ts:327-347).
• publish needs --project-id. No command lists projects or returns their ids.
• sync always covers every project in the workspace. There is no per-project filter.
• Only sync, run and schedule read .env, each from its own folder. publish, static-site access and streamlit publish don't read it.
• Nothing creates a starter app. A static app is just a folder that publish uploads.

Tasks

• Release @deepnote/cli, @deepnote/cloud and @deepnote/mcp with publish, static-site access and streamlit publish, once feat(cli): add deepnote streamlit publish #466 merges.
• Add -o json to publish, static-site access and streamlit publish:
  • Static: {url, projectId, apiAccess, filesUploaded, pruned}
  • Streamlit: {appId, url, status}
  • A divergence ("Deepnote changed these files since the last sync") gets its own error code or exit code, so callers can offer "sync first" or "force".
• Look up DEEPNOTE_TOKEN in .env the same way for every command that needs a token: the command's folder first, then parent folders up to the sync root. The missing-token error should tell the user to add DEEPNOTE_TOKEN to .env.
• Make --project-id optional for publish and streamlit publish. When the folder is inside a synced project, take the id from .deepnote-sync.json or from the .deepnote file's project id.
• Add deepnote projects list -o json, returning id, name, folder path and URL.
• Add deepnote sync --project <id|path> to sync a single project. This is separate from the speed-up in feat(cli,cloud): sync projects concurrently and retry rate-limited requests #535.
• Add deepnote app init <dir> --template static|ts|streamlit, which creates a starter app. The TS template builds to a folder that publish can upload. The extension and agents will share these templates.
• Update skills/deepnote/references/{cli-publish,cli-sync,apps}.md and docs/, as AGENTS.md requires.

Done when

An agent with no TTY and only a .env file can do all of this without running --help or parsing text:

1. Create an app.
2. Sync one project.
3. Publish the app.
4. Get the URL back as JSON.

Unblocks the vscode-deepnote work on agent setup and on sync and publish buttons.

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