[BUG] Inconsistencies between Claude Code CLI and Claude Code in Desktop app: MCPs, Skills, async usage, and opusplan mode

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?

I'm experiencing several incompatibility issues between the Claude Code CLI and Claude Code inside the Desktop app:

1. The Claude Code CLI configuration does not load inside the Claude Code instance running in the Desktop app. MCPs configured in the CLI also do not load there.
2. It appears that I need to configure Skills separately (in a different way) to make them work inside the Claude Code in the Desktop app. MCPs also do not integrate between the two environments.
3. I cannot use the Claude Code CLI and the Claude Code in the Desktop app asynchronously, because the two instances do not share state/context — things are not async.
4. To start using Claude Code, I have to configure MCPs and Skills differently for each environment. This duplicates configuration work and makes the experience bad for me.
5. When I use the opusplan model, it works, but it exits the mode afterwards. Every time I want Opus to create a plan and Sonnet to execute it, I have to run /model opusplan again before each new plan.

What Should Happen?

• MCP and Skills configuration should be shared/integrated between the Claude Code CLI and the Claude Code inside the Desktop app, with no need to configure them twice.
• It should be possible to use the CLI and the Desktop app asynchronously, with state synchronized between them.
• The opusplan mode should persist across plan/execute cycles, without requiring me to re-enable it via /model opusplan every time a new plan is created.

Error Messages/Logs

Steps to Reproduce

1. Configure MCPs and Skills in the Claude Code CLI.
2. Open Claude Code inside the Desktop app and observe that the MCPs and Skills configured for the CLI are not available there.
3. Try to use the CLI and the Desktop app simultaneously in an asynchronous workflow — observe that the two instances are not synchronized.
4. In the CLI, run /model opusplan. Let Opus create a plan and Sonnet execute it.
5. Start a new plan: notice that opusplan mode has been deactivated and /model opusplan must be run again before each new plan.

Claude Model

Other

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

2.1.117 (Claude Code)

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Other

Additional Information

_No response_