MCP server registered via 'claude mcp add' not surfacing tools in conversational interface when claude.ai web connectors are also present

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?

A locally-registered MCP server shows ✓ Connected in claude mcp list
and claude mcp get, but its tools are completely invisible to the
Claude Code conversational interface. Only tools from claude.ai web
connectors are surfaced. The two tool namespaces do not merge.

Specifically: registered @microsoft/dataverse via claude mcp add
with stdio transport. claude mcp list confirms ✓ Connected. When
asked conversationally to use the dataverse MCP server, Claude Code
reports only CDATA/QBO web connector tools are available and states
no Dataverse connection is configured.

What Should Happen?

Tools from locally-registered MCP servers (via claude mcp add) and
tools from claude.ai web connectors should be available in the same
conversational tool context simultaneously.

Error Messages/Logs

No error message is produced. claude mcp list output:

dataverse: npx -y @microsoft/dataverse mcp https://org4a756e0c.crm.dynamics.com - ✓ Connected

claude mcp get dataverse output:

dataverse:
  Scope: Local config (private to you in this project)
  Status: ✓ Connected
  Type: stdio
  Command: npx
  Args: -y @microsoft/dataverse mcp https://org4a756e0c.crm.dynamics.com
  Environment:

Secondary issue — Claude Desktop produces this error with the same package:
MCP BGF-Dataverse: Unexpected token 'w', "warn: Mode"... is not valid JSON
(npm warning messages written to stdout break Claude Desktop's stdio JSON-RPC parser)

Steps to Reproduce

1. Have one or more claude.ai web connectors active (CDATA QBO BGF

and Microsoft 365 were active in our case)

1. Create a valid auth profile for the target MCP server:

npx @microsoft/dataverse auth create --applicationId <appId>
--clientSecret <secret> --tenant <tenantId>
--environment https://org4a756e0c.crm.dynamics.com
(confirms: Default organization: BGF Dev-Test-Run)

1. Register the MCP server:

claude mcp add dataverse -t stdio -- npx -y @microsoft/dataverse
mcp https://org4a756e0c.crm.dynamics.com

1. Verify: claude mcp list → shows ✓ Connected
2. Restart Claude Code
3. Ask conversationally: "Using the dataverse MCP server, list

available tables in the Dataverse environment."

1. Claude Code responds using only CDATA web connector tools and

reports no Dataverse connection available.

Claude Model

None

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

2.1.122 (Claude Code)

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

PowerShell

Additional Information

Auth loop side effect: After registering the dataverse MCP server,
Claude Code entered a Microsoft authentication loop presenting the
Application (client) ID (d8d9280f-...) as the sign-in username rather
than prompting for user credentials. This persisted across restarts and
destabilized the Claude Code session. See attached screenshot.

<img width="845" height="1020" alt="Image" src="https://github.com/user-attachments/assets/e69380f7-25d4-4ed6-a118-6704ea5ae466" />