[BUG] MCP server tools discovered but not accessible via ToolSearch in Claude Code

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?

Claude Code successfully connects to MCP servers, discovers tools, and completes authentication, but the discovered tools are not accessible through the ToolSearch mechanism, making them unusable

What Should Happen?

Claude should be able to access the MCP servers

Error Messages/Logs

Steps to Reproduce

Start the MCP server and try and access if via the Claude code window.

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.81

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Windows Terminal

Additional Information

Configuration
mcp.json located at: C:\Users\[user]\AppData\Roaming\Code\User\mcp.json

{
"servers": {
"my-mcp-server-2cebe382": {
"url": "https://mcp.atlassian.com/v1/sse",
"type": "http"
},
"my-mcp-server-713fa1d6": {
"url": "https://api.githubcopilot.com/mcp",
"type": "http",
"gallery": "https://api.mcp.github.com/2025-09-15/v0/servers/ab12cd34-5678-90ef-1234-567890abcdef",
"version": "0.13.0"
}
},
"inputs": []
}
Observed Behavior
MCP Server Logs (Atlassian):

2026-03-24 08:01:03.983 [info] Connection state: Running
2026-03-24 08:01:04.518 [info] Discovered authorization server metadata at https://mcp.atlassian.com/.well-known/oauth-authorization-server
2026-03-24 08:01:06.165 [info] Discovered 31 tools
2026-03-24 08:14:23.896 [info] Found 1 sessions for scopes:
Authentication: ✅ Working (OAuth sessions found)

Tool Discovery: ✅ Working (31 + 44 tools discovered)

Tool Access: ❌ Not Working

When Claude attempts to search for MCP tools using ToolSearch:

ToolSearch query: "select:getJiraIssue,searchJiraIssuesUsingJql,getConfluencePage"
Result: "No matching deferred tools found"
All search attempts fail, including:

Direct tool name selection: select:toolName
Keyword searches: jira, confluence, atlassian
Generic searches: issue, page, search
Expected Behavior
Once MCP servers discover tools and authentication succeeds, those tools should be:

Available via ToolSearch
Callable by Claude to execute user requests
Listed in the available tools registry
Known Tool Names (from Atlassian MCP docs)
According to official documentation, the Atlassian MCP should expose 25+ tools including:

getJiraIssue, searchJiraIssuesUsingJql, createJiraIssue
getConfluencePage, searchConfluenceUsingCql, createConfluencePage
And 19 more tools
None of these are accessible despite being discovered.

Impact
Users cannot leverage MCP server integrations within Claude Code, limiting the usefulness of the MCP feature for Jira, Confluence, GitHub, and other services.

Reproduction Steps
Configure MCP servers in mcp.json
Restart VS Code / Claude Code
Observe in Output panel that servers connect and tools are discovered
Ask Claude to use an MCP tool (e.g., "Search for Jira issues assigned to me")
Observe that ToolSearch returns "No matching deferred tools found"
Additional Context
The Atlassian VS Code extension (atlascode v4.0.27) is also installed but is separate from the MCP integration
Issue affects multiple MCP servers (not just Atlassian)
No error messages appear in logs - discovery appears successful
Would you like me to adjust anything in this issue description before you submit it?