[Bug] ctx Tools Only Partially Working with Multiple MCPs in Cursor

[Crock0il]

1. Environment:

• OS: Arch Linux
• ctx version: 1.27.1
• Installation location: $HOME/.local/bin (it is included in $PATH)
• Installation method: Direct installation (not using PHAR)
• PHP: Not installed on system

2. Issue Description:

When ctx is the ONLY MCP in configuration, all tools work fine. However, when multiple MCPs are configured, only mcp_ctx_context remains accessible while all other ctx tools (mcp_ctx_file_read, mcp_ctx_file_info, mcp_ctx_directory_list, etc.) return "Tool not found" errors.

3. Key Observations:

• ctx works properly alone: When ctx is the only MCP in mcp.json, all tools function correctly
• Conflict with multiple MCPs: Problems occur only when multiple MCPs are configured together
• Only affects ctx: Other MCPs continue to work properly even when multiple MCPs (including ctx) are configured
• Partial functionality: Only mcp_ctx_context works when multiple MCPs are present; all other ctx tools fail
• Only in Cursor: ctx functions outside of AI assistant integration work fine

4. Reproduction Steps:

• Configure ctx as the only MCP in Cursor's mcp.json - all tools work correctly
• Add additional MCPs to mcp.json
• After adding multiple MCPs, only mcp_ctx_context works, while all other ctx tools fail with "Tool with ID X not found"

5. Expected Behavior:

All ctx tools (file_read, directory_list, etc.) should continue working even when multiple MCPs are configured in Cursor.

6. Actual Behavior:

Only the mcp_ctx_context tool functions correctly when multiple MCPs are present. All other ctx tools return "Tool not found" errors.

Generated this bug report with AI assistant hehe
Here's what my mcp.json looks like right now
{
"mcpServers": {
"ctx": {
"command": "ctx",
"args": [
"server",
"-c",
"/home/crock0il/Projects/python_api_tests"
]
},
"testit": {
"command": "/home/crock0il/Projects/testit_mcp/.venv/bin/python",
"args": [
"/home/crock0il/Projects/testit_mcp/testit_mcp.py"
],
"env": {
"TESTIT_TOKEN": "********",
"TESTIT_BASE_URL": "********",
"TRANSPORT": "stdio"
}
}
}
}

And here's a couple of screenshots for good measure