[BUG] MCP Tools Not Accessible via MCPSearch Despite Server Connection Description

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?

Bug Report: MCP Tools Not Accessible via MCPSearch Despite Server Connection

Description

MCP server tools are not being loaded/discovered by the MCPSearch tool, even though the MCP servers show as "✓ Connected" in claude mcp list. This makes MCP tools completely unusable within Claude Code sessions.

Steps to Reproduce

1. Add an MCP server using claude mcp add <name> <command>
2. Verify server is connected with claude mcp list (shows ✓ Connected)
3. Try to discover tools using MCPSearch with various queries:

• MCPSearch("confluence")
• MCPSearch("jira")
• MCPSearch("select:mcp__jira__confluence_fetch_page")

1. All queries return no results

Expected Behavior

MCPSearch should discover and load the tools exposed by connected MCP servers, allowing them to be invoked.

Actual Behavior

MCPSearch returns no results (<system>Tool ran without output or errors</system>) despite servers being connected.

Environment

• Platform: Windows (win32)
• Claude Code: VSCode Extension
• MCP Server: Custom JIRA/Confluence server (stdio transport)
• Server Command: node c:/abanoub/scripts/jira-mcp-server/dist/index.js
• Tools Expected: jira_fetch_ticket, jira_create_subtask, confluence_fetch_page

MCP Server Configuration

The MCP server is properly configured and defines 3 tools:

const TOOLS = [
    {
        name: 'jira_fetch_ticket',
        description: 'Fetch details of a JIRA ticket by its key (e.g., OP-6681)',
        inputSchema: { /* ... */ }
    },
    {
        name: 'jira_create_subtask',
        description: 'Create a subtask under a parent JIRA ticket',
        inputSchema: { /* ... */ }
    },
    {
        name: 'confluence_fetch_page',
        description: 'Fetch content from a Confluence page by ID or URL',
        inputSchema: { /* ... */ }
    }
];

Attempts to Resolve

• ✗ Reloaded VSCode
• ✗ Restarted MCP server (claude mcp restart jira)
• ✗ Added duplicate servers with different names in same session
• ✗ Tried various MCPSearch query patterns (keywords and direct selection)
• ✗ Verified server code has tools properly defined

Additional Notes

• claude mcp list consistently shows servers as "✓ Connected"
• Multiple MCP server instances (4 total) all show as connected but tools still not accessible
• No claude mcp invoke command exists to test tools directly via CLI
• Issue persists across multiple MCP server instances added in the same session
• The MCP server itself appears to be functioning correctly (no errors on startup)

Impact

This issue makes MCP integration completely non-functional, preventing users from leveraging custom MCP servers within Claude Code.

What Should Happen?

Bug Report: MCP Tools Not Accessible via MCPSearch Despite Server Connection

Description

MCP server tools are not being loaded/discovered by the MCPSearch tool, even though the MCP servers show as "✓ Connected" in claude mcp list. This makes MCP tools completely unusable within Claude Code sessions.

Steps to Reproduce

1. Add an MCP server using claude mcp add <name> <command>
2. Verify server is connected with claude mcp list (shows ✓ Connected)
3. Try to discover tools using MCPSearch with various queries:

• MCPSearch("confluence")
• MCPSearch("jira")
• MCPSearch("select:mcp__jira__confluence_fetch_page")

1. All queries return no results

Expected Behavior

MCPSearch should discover and load the tools exposed by connected MCP servers, allowing them to be invoked.

Actual Behavior

MCPSearch returns no results (<system>Tool ran without output or errors</system>) despite servers being connected.

Environment

• Platform: Windows (win32)
• Claude Code: VSCode Extension
• MCP Server: Custom JIRA/Confluence server (stdio transport)
• Server Command: node c:/abanoub/scripts/jira-mcp-server/dist/index.js
• Tools Expected: jira_fetch_ticket, jira_create_subtask, confluence_fetch_page

MCP Server Configuration

The MCP server is properly configured and defines 3 tools:

const TOOLS = [
    {
        name: 'jira_fetch_ticket',
        description: 'Fetch details of a JIRA ticket by its key (e.g., OP-6681)',
        inputSchema: { /* ... */ }
    },
    {
        name: 'jira_create_subtask',
        description: 'Create a subtask under a parent JIRA ticket',
        inputSchema: { /* ... */ }
    },
    {
        name: 'confluence_fetch_page',
        description: 'Fetch content from a Confluence page by ID or URL',
        inputSchema: { /* ... */ }
    }
];

Attempts to Resolve

• ✗ Reloaded VSCode
• ✗ Restarted MCP server (claude mcp restart jira)
• ✗ Added duplicate servers with different names in same session
• ✗ Tried various MCPSearch query patterns (keywords and direct selection)
• ✗ Verified server code has tools properly defined

Additional Notes

• claude mcp list consistently shows servers as "✓ Connected"
• Multiple MCP server instances (4 total) all show as connected but tools still not accessible
• No claude mcp invoke command exists to test tools directly via CLI
• Issue persists across multiple MCP server instances added in the same session
• The MCP server itself appears to be functioning correctly (no errors on startup)

Impact

This issue makes MCP integration completely non-functional, preventing users from leveraging custom MCP servers within Claude Code.

Error Messages/Logs

Steps to Reproduce

Bug Report: MCP Tools Not Accessible via MCPSearch Despite Server Connection

Description

MCP server tools are not being loaded/discovered by the MCPSearch tool, even though the MCP servers show as "✓ Connected" in claude mcp list. This makes MCP tools completely unusable within Claude Code sessions.

Steps to Reproduce

1. Add an MCP server using claude mcp add <name> <command>
2. Verify server is connected with claude mcp list (shows ✓ Connected)
3. Try to discover tools using MCPSearch with various queries:

• MCPSearch("confluence")
• MCPSearch("jira")
• MCPSearch("select:mcp__jira__confluence_fetch_page")

1. All queries return no results

Expected Behavior

MCPSearch should discover and load the tools exposed by connected MCP servers, allowing them to be invoked.

Actual Behavior

MCPSearch returns no results (<system>Tool ran without output or errors</system>) despite servers being connected.

Environment

• Platform: Windows (win32)
• Claude Code: VSCode Extension
• MCP Server: Custom JIRA/Confluence server (stdio transport)
• Server Command: node c:/abanoub/scripts/jira-mcp-server/dist/index.js
• Tools Expected: jira_fetch_ticket, jira_create_subtask, confluence_fetch_page

MCP Server Configuration

The MCP server is properly configured and defines 3 tools:

const TOOLS = [
    {
        name: 'jira_fetch_ticket',
        description: 'Fetch details of a JIRA ticket by its key (e.g., OP-6681)',
        inputSchema: { /* ... */ }
    },
    {
        name: 'jira_create_subtask',
        description: 'Create a subtask under a parent JIRA ticket',
        inputSchema: { /* ... */ }
    },
    {
        name: 'confluence_fetch_page',
        description: 'Fetch content from a Confluence page by ID or URL',
        inputSchema: { /* ... */ }
    }
];

Attempts to Resolve

• ✗ Reloaded VSCode
• ✗ Restarted MCP server (claude mcp restart jira)
• ✗ Added duplicate servers with different names in same session
• ✗ Tried various MCPSearch query patterns (keywords and direct selection)
• ✗ Verified server code has tools properly defined

Additional Notes

• claude mcp list consistently shows servers as "✓ Connected"
• Multiple MCP server instances (4 total) all show as connected but tools still not accessible
• No claude mcp invoke command exists to test tools directly via CLI
• Issue persists across multiple MCP server instances added in the same session
• The MCP server itself appears to be functioning correctly (no errors on startup)

Impact

This issue makes MCP integration completely non-functional, preventing users from leveraging custom MCP servers within Claude Code.

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.0.47 (Claude Code)

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

VS Code integrated terminal

Additional Information

_No response_