Desktop app clobbers CLI plugin MCP servers when viewing shared session

Bug Description

When a Claude Code CLI session with active plugin-managed MCP servers (e.g., the Telegram plugin) is opened/viewed in the Claude Desktop Mac app, the Desktop app calls replaceRemoteMcpServers and overwrites the session's MCP server list with its own set — dropping any CLI-managed plugin servers that aren't in the Desktop app's configuration.

This kills the plugin MCP server connection and requires the user to run /mcp in the CLI to reconnect.

Steps to Reproduce

1. Start a Claude Code CLI session with the Telegram plugin enabled (enabledPlugins: { "telegram@claude-plugins-official": true })
2. Confirm the Telegram MCP server is connected and working (send/receive messages)
3. Open the same session in the Claude Desktop Mac app
4. Return to the CLI — the Telegram MCP tools are gone (No such tool available: mcp__plugin_telegram_telegram__reply)
5. Run /mcp to reconnect

Evidence from Logs

Desktop app log (~/Library/Logs/Claude/main.log) shows the moment the session was opened in the Desktop app:

17:56:42 [info] [CCD] LocalSessions.replaceEnabledMcpTools: sessionId=local_f1a8f1be-..., toolCount=46
17:56:43 [info] [CCD] LocalSessions.replaceRemoteMcpServers: sessionId=local_f1a8f1be-..., serverCount=3
17:56:43 [info] [CCD] [replaceRemoteMcpServers] Calling SDK with 9 total servers {
  serverNames: ['Gmail', 'Google Calendar', 'gdrive', 'Claude in Chrome', 'mcp-registry', 'Claude Preview', 'Control Chrome', 'docker', 'scheduled-tasks']
}

Note: Telegram is absent from the server list. The Desktop app replaced the session's MCP config with its own, which doesn't include CLI plugin-managed servers.

Plugin source (server.ts lines 564-578) confirms the mechanism — the Telegram MCP server listens for stdin EOF/close and calls shutdown():

process.stdin.on('end', shutdown)
process.stdin.on('close', shutdown)

When the Desktop app replaces the MCP servers, the CLI's stdio pipe to the Telegram process is severed, triggering a clean shutdown.

Expected Behavior

The Desktop app should merge its MCP servers with any existing CLI plugin-managed servers rather than replacing them, or at minimum preserve CLI plugin servers when viewing a shared session.

Environment

• macOS (Darwin 24.6.0)
• Claude Code CLI with Telegram plugin (telegram@claude-plugins-official)
• Claude Desktop Mac app
• Reproducible 100% of the time

Workaround

Run /mcp in the CLI after the Desktop app disconnects the plugin server. Avoid opening active CLI sessions in the Desktop app when plugin MCP servers need to stay connected.