[BUG] Claude Code Desktop does not sync settings, MCPs, or skills from Claude Code CLI

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Claude Code Desktop (Windows) does not read or sync my existing Claude Code CLI configuration. Settings I've customized in the CLI are completely ignored by the Desktop app, and there seems to be no shared configuration layer between them.

Specifically:

1. settings.json is not respected. I've configured model variants in my CLI settings.json (e.g. Opus and Sonnet with the 1M context window). The Desktop app ignores these overrides and uses default models.
2. Per-project MCPs are not loaded. MCP servers I've configured per-project in the CLI are not available in Desktop. I'd have to reconfigure everything globally to use them.
3. Skills don't carry over. Skills I have loaded per-project in the CLI are not available in Desktop either.
4. /model opusplan behaves inconsistently. It can be selected on Desktop, but after a plan is executed, re-entering plan mode does not switch back to Opus — it stays on Sonnet. On the CLI this cycle works correctly.

The overall result: CLI and Desktop feel like two disconnected products rather than two interfaces of the same tool, which breaks any project-based workflow built around the CLI.

What Should Happen?

Claude Code Desktop should share configuration with Claude Code CLI, including:

• Respecting settings.json (model overrides, context window variants, etc.)
• Loading project-scoped MCP servers configured via the CLI
• Loading project-scoped skills configured via the CLI
• Keeping /model opusplan behavior consistent with the CLI (switch back to Opus when re-entering plan mode)

Error Messages/Logs

No error is shown. The Desktop app silently ignores CLI configuration.

Steps to Reproduce

1. On Windows, install and configure Claude Code CLI with a customized settings.json (e.g. set Opus and Sonnet to their 1M context window variants), project-scoped MCP servers, and project-scoped skills.
2. Confirm everything works as expected in the CLI inside the project directory.
3. Open the same project in Claude Code Desktop.
4. Observe:

• settings.json overrides are not applied (default models are used).
• Project MCP servers are not available.
• Project skills are not available.

1. Run /model opusplan in Desktop, create a plan, and execute it. Re-enter plan mode and observe the model does not switch back to Opus (stays on Sonnet).

Claude Model

Not sure / Multiple models

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

2.1.118 (Claude Code)

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

PowerShell

Additional Information

This is a significant workflow blocker for users coming from the CLI. opusplan in particular is important because using Opus for everything consumes session limits very quickly — the Opus-for-planning / Sonnet-for-execution split is what makes daily work sustainable, and losing it on Desktop makes the app much harder to adopt as a primary tool.