[BUG] Atlassian MCP Server Tools Not Available in Claude Code 2.0.10 Conversations Despite Successful Connection

Found 3 possible duplicate issues:

1. https://github.com/anthropics/claude-code/issues/2682
2. https://github.com/anthropics/claude-code/issues/8407
3. https://github.com/anthropics/claude-code/issues/3426

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🤖 Generated with Claude Code

I don't believe this is a dup. I have the same problem, just started today.

I'm getting the message in the log:

````
{
"error": "Connection failed: SSE MCP servers are currently not supported in native builds.",
"timestamp": "2025-10-09T13:24:20.450Z",
"sessionId": "32d777bf-61ce-4f6d-ae6b-56a5291b903f",
"cwd": "/Users/mrunkel/Herd/kautionskonto"
},

````
After moving the native client out of the way and running the nodejs claude, it works fine.

So, the question becomes, why aren't SSE MCP server support in the native build any longer?

Yes also started today, a few hours ago even. Same question as above, why did it stop working all of a sudden?

I ran into this yesterday with some other SSE MCP servers and am wondering why it's unsupported.

I rewrote my MCP-server to use HTTP stream instead of (the deprecated) SSE. The server seems to work fine - but 2.0.22 (Claude Code) cannot use it. :-(

is there any fix for this - use the Atlassian MCP in CC - works fine still in terminal just no longer in vscode extension

I can just use with the instructions from doc for Atlassian as below

claude mcp add --transport sse atlassian https://mcp.atlassian.com/v1/sse

I can confirm this issue persists in v2.0.54 on macOS (Darwin 25.1.0).

My Configuration:

• MCP Server: serena (semantic code navigation)
• Server shows "✓ Connected" in /mcp UI
• Server logs confirm successful startup with 23 tools registered
• ListMcpResourcesTool returns empty array
• Tools not visible in /context output
• Tools not available in AI's function set

Evidence:
Server logs show successful initialization:

INFO Starting MCP server with 23 tools: ['list_dir', 'find_file', 'search_for_pattern', 
'get_symbols_overview', 'find_symbol', 'find_referencing_symbols', ...]
INFO MCP server lifetime setup complete

But from the AI perspective: tools are completely unavailable despite the connection.

This confirms the bug affects:

• Multiple MCP servers (Atlassian, serena, caelum servers)
• Multiple Claude Code versions (v2.0.10 → v2.0.54)
• Persists across restarts and new sessions

Related upstream issue: https://github.com/oraios/serena/issues/780

Already fixed？

Docker MCP Gateway Confirms Same Issue

Adding another data point: This same issue affects Docker MCP Gateway with multiple servers tested.

Quick Summary

• ✅ Gateway connects: ✓ Connected in claude mcp list
• ✅ Tools properly formatted: MCP-compliant naming with double underscores
• ✅ MCP protocol working: handshake and tools/list successful
• ❌ Tools not exposed: Claude Code assistant can't access them

Servers Tested via Docker Gateway

• github-official (40 tools)
• cloudflare-docs (2 tools)

All show identical behavior to the Atlassian MCP server issue.

Configuration

{
  "mcpServers": {
    "MCP_DOCKER": {
      "command": "docker",
      "args": ["mcp", "gateway", "run", "--secrets", ".env.mcp", "--servers", "cloudflare-docs"],
      "type": "stdio"
    }
  }
}

Impact

This prevents access to 200+ MCP servers available through Docker MCP Gateway catalog, significantly limiting Claude Code's extensibility.

Full details and test results: https://github.com/anthropics/claude-code/issues/12164#issuecomment-3604075563

This confirms the issue is not specific to Atlassian but affects MCP tool exposure generally in Claude Code.

This issue has been inactive for 30 days. If the issue is still occurring, please comment to let us know. Otherwise, this issue will be automatically closed in 30 days for housekeeping purposes.

This is still an issue, but I managed to get a workaround working.

in terminal chat, type:
/mcp
Choose rovo and view tools
choose the tool you need (in my case "Retrieve Jira issue")
Take the whole box and copy it:

╭──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ Retrieve Jira issue (rovo) [read-only]                                                                                                                               │
│                                                                                                                                                                      │
│ Tool name: getJiraIssue                                                                                                                                              │
│ Full name: mcp__rovo__getJiraIssue                                                                                                                                   │
│                                                                                                                                                                      │
│ Description:                                                                                                                                                         │
│ Get a Jira issue by issue id or key.                                                                                                                                 │
│                                                                                                                                                                      │
│ Parameters:                                                                                                                                                          │
│   • cloudId (required): string - Unique identifier for an Atlassian Cloud instance in the form of a UUID. Can also be a site URL or extracted from Atlassian URLs -  │
│   for example, from https://yoursite.atlassian.net/wiki/.... If not working, use the 'getAccessibleAtlassianResources' tool to find accessible Cloud IDs.            │
│   • issueIdOrKey (required): string - Issue id or key can be used to uniquely identify an existing issue.                                                            │
│   Issue id is a numerical identifier. An example issue id is 10000.                                                                                                  │
│   Issue key is formatted as a project key followed by a hyphen '-' character and then followed by a sequential number.                                               │
│   An example issue key is ISSUE-1.                                                                                                                                   │
│   • fields: array                                                                                                                                                    │
│   • fieldsByKeys: boolean                                                                                                                                            │
│   • expand: string                                                                                                                                                   │
│   • properties: array                                                                                                                                                │
│   • updateHistory: boolean                                                                                                                                           │
│   • failFast: boolean                                                                                                                                                │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

paste that into that and ask the LLM to use that tool.

The chat is able to use that tool going forward in that session

This issue has been automatically closed due to 60 days of inactivity. If you're still experiencing this issue, please open a new issue with updated information.

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