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claude-code - 💡(How to fix) Fix [BUG] Inconsistencies between Claude Code CLI and Claude Code in Desktop app: MCPs, Skills, async usage, and opusplan mode [1 participants]

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anthropics/claude-code#52154•Fetched 2026-04-23 07:35:12
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Error Message

Error Messages/Logs

Root Cause

  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.
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Preflight Checklist

  • I have searched existing issues and this hasn't been reported yet
  • This is a single bug report (please file separate reports for different bugs)
  • 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

extent analysis

TL;DR

The most likely fix involves synchronizing the configuration and state between the Claude Code CLI and the Desktop app, potentially through a shared configuration file or API.

Guidance

  • Investigate the possibility of using a shared configuration file that can be accessed by both the CLI and the Desktop app to synchronize MCPs and Skills configurations.
  • Explore the Anthropic API documentation to see if there are any endpoints or methods that can be used to synchronize state between the CLI and the Desktop app.
  • Consider implementing a workaround that involves running a script to configure the Desktop app with the same MCPs and Skills as the CLI before starting a new plan.
  • Look into the opusplan mode documentation to see if there are any options or flags that can be used to make the mode persist across plan/execute cycles.

Example

No code snippet is provided as the issue does not contain enough information about the specific APIs or functions being used.

Notes

The issue seems to be related to the lack of synchronization between the CLI and the Desktop app, and the fact that the opusplan mode does not persist across plan/execute cycles. Without more information about the underlying APIs and functions, it is difficult to provide a more specific solution.

Recommendation

Apply workaround: The issue is likely due to a design limitation or missing feature, and a workaround may be the best solution until a proper fix is implemented. A potential workaround could involve using a shared configuration file or script to synchronize the configuration and state between the CLI and the Desktop app.

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claude-code - 💡(How to fix) Fix [BUG] Inconsistencies between Claude Code CLI and Claude Code in Desktop app: MCPs, Skills, async usage, and opusplan mode [1 participants]