Fix: Enable RTC mode with jupyter-collaboration to prevent WebSocket disconnections

[delphos-mike]

Problem

When using jupyter-mcp-server 0.17.0 as a Jupyter Server Extension with jupyter-collaboration, MCP tools fall back to "file mode" instead of using RTC (Real-Time Collaboration) mode, causing WebSocket disconnections in the JupyterLab UI.

Symptoms

• User executes cells successfully from JupyterLab UI
• MCP client (Claude Code) modifies/executes cells via MCP tools (works fine)
• After MCP modifications, user's UI becomes unresponsive
• Cells don't execute from UI, execution counter doesn't update
• Browser refresh required to restore UI functionality
• Kernel stays alive but WebSocket connection is broken

Environment

• jupyter-mcp-server 0.17.0 (Jupyter Server Extension mode)
• jupyterlab 4.4.1
• jupyter-collaboration 4.0.2
• datalayer-pycrdt 0.12.17
• Python 3.13.7
• Claude Code as MCP client

MCP Configuration

```json
{
"mcpServers": {
"jupyter": {
"command": "npx",
"args": ["mcp-remote", "http://127.0.0.1:8888/mcp"]
}
}
}
```

Server Logs

```
[INFO] Notebook not open, using file mode
[INFO] Wrote outputs to cell in
[INFO] Out-of-band changes. Overwriting the content in room json:notebook:
```

The "Out-of-band changes" message indicates MCP wrote to the file directly, bypassing the Y.js collaboration layer, which breaks the UI's WebSocket connection.

Root Cause

1. MCP tools access collaboration via `serverapp.web_app.settings.get("yroom_manager")`
2. jupyter-collaboration never adds `yroom_manager` to `web_app.settings`
3. YDocExtension stores it as `self.ywebsocket_server` but doesn't expose it in settings
4. When yroom_manager lookup returns None, tools fall back to direct file writes
5. Direct file writes bypass Y.js CRDT layer → "Out-of-band changes" → WebSocket disconnect

Solution

Access ywebsocket_server via the extension_manager:

```python
serverapp.extension_manager.extension_points['jupyter_server_ydoc'].app.ywebsocket_server
```

Also fixed DocumentRoom API - access document via `room._document` instead of calling non-existent `get_jupyter_ydoc()` method.

Impact

✅ MCP now uses true RTC mode when jupyter-collaboration is available
✅ No more WebSocket disconnections after MCP cell modifications
✅ UI stays responsive - no browser refresh required
✅ Enables true simultaneous editing between MCP clients and human users
✅ Works with Claude Code, VS Code, Cursor, and other MCP clients

Files Changed

• `execute_cell_tool.py`
• `overwrite_cell_source_tool.py`
• `insert_cell_tool.py`
• `insert_execute_code_cell_tool.py`
• `delete_cell_tool.py`

Testing

Verified with:

• JupyterLab 4.4.1 + jupyter-collaboration 4.0.2 + datalayer-pycrdt 0.12.17
• jupyter-mcp-server 0.17.0 as Jupyter Server Extension
• Claude Code as MCP client (npx mcp-remote transport)
• Confirmed MCP cell modifications no longer break UI WebSocket
• Confirmed execution from both MCP and UI works simultaneously without refresh
• Server logs now show "Notebook is open, using RTC mode" instead of "file mode"

[echarles]

LGTM Thx @delphos-mike - Looks like the structural changes to the ipynb need to be propagated via RTC if the extension is installed - that sounds logic to me.