System prompt MCP folder path is inconsistent with actual MCP storage location for multi-repo workspaces

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1

Where does the bug appear (feature/product)?

Cursor IDE

Describe the Bug

Bug Description

When using a multi-repo workspace file (e.g., my-workspace.code-workspace), the system prompt’s <mcp_file_system> section points to an MCP folder path based on the first workspace folder, but Cursor actually stores MCPs under a path based on the workspace filename.

Steps to Reproduce

  1. Create a workspace file that includes multiple repos (e.g., my-multi-repo-workspace.code-workspace containing repo1, repo2, etc.)
  2. Open the workspace in Cursor
  3. Configure an MCP server in ~/.cursor/mcp.json
  4. Observe the system prompt generated for AI agents

Expected Behavior

The system prompt’s MCP folder path should match where MCPs are actually stored:

~/.cursor/projects/Users-username-path-to-workspace-filename/mcps

Actual Behavior

The system prompt says:

The MCP tool descriptors live in the /Users/username/.cursor/projects/Users-username-path-to-repo1/mcps folder.

But the MCPs are actually stored at:

/Users/username/.cursor/projects/Users-username-path-to-workspace-file/mcps

Impact

AI agents following the system prompt path will look in the wrong folder and incorrectly conclude that MCP servers are not loaded, even when they are functioning correctly.

Environment

  • macOS
  • Cursor (latest version)
  • Multi-repo workspace file

Workaround

Manually check all ~/.cursor/projects/*/mcps/ folders instead of trusting the path in the system prompt.

Steps to Reproduce

  1. Create a workspace file that includes multiple repos (e.g., my-multi-repo-workspace.code-workspace containing repo1, repo2, etc.)
  2. Open the workspace in Cursor
  3. Configure an MCP server in ~/.cursor/mcp.json
  4. Observe the system prompt generated for AI agents

Operating System

MacOS

Current Cursor Version (Menu → About Cursor → Copy)

Version: 2.3.41 (Universal)
VSCode Version: 1.105.1
Commit: 2ca326e0d1ce10956aea33d54c0e2d8c13c58a30
Date: 2026-01-16T19:14:00.150Z
Electron: 37.7.0
Chromium: 138.0.7204.251
Node.js: 22.20.0
V8: 13.8.258.32-electron.0
OS: Darwin arm64 25.2.0

Does this stop you from using Cursor

Sometimes - I can sometimes use Cursor

3

Hey, thanks for the detailed report with repro steps.

This looks like a known issue with resolving MCP paths in the project context, and the team is already working on a fix. For now, you can use the workaround you described and manually check all the ~/.cursor/projects/*/mcps/ folders.