claude.ai Atlassian MCP connector: connection closes immediately after handshake, tools never listed

Claude Code version: 2.1.205 (native install, macOS)

What happened

The claude.ai Atlassian MCP connector (Jira/Confluence, added via the org-level Directory > Connectors UI, proxied through mcp-proxy.anthropic.com) shows as ✔ Connected in claude mcp list, but no Atlassian/Jira/Confluence tools are ever exposed to a Claude Code session. This reproduced across:

• Multiple fresh conversations
• A full restart of the Claude Code desktop app
• Several minutes and multiple retries after the connector was (re-)authorized

The connector had reportedly been connected for several weeks prior to this report, ruling out "just wait for it to propagate."

Evidence from per-session MCP debug logs

~/Library/Caches/claude-cli-nodejs/<project>/mcp-logs-claude-ai-Atlassian/*.jsonl shows the same failure on 3 separate connection attempts (3 different sessionIds):

Initializing claude.ai proxy transport for server mcpsrv_013rc1WvXe3LTmj6iDcmLfMF
Using claude.ai proxy at https://mcp-proxy.anthropic.com/v1/mcp/mcpsrv_013rc1WvXe3LTmj6iDcmLfMF
claude.ai proxy transport created successfully
Starting connection with timeout of 30000ms
Successfully connected (transport: claudeai-proxy) in ~900-1400ms
Connection established with capabilities: {"hasTools":true,"hasPrompts":false,"hasResources":true,"hasResourceSubscribe":false,"serverVersion":{"name":"atlassian-mcp-server","version":"1.0.0"}}
CLAUDEAI-PROXY connection closed after 0s (cleanly)
Cleared connection cache for reconnection

The server correctly advertises "hasTools":true, but the proxy connection is torn down immediately after the handshake, before any tools/list call appears to complete, and the promised reconnect never succeeds in surfacing tools to the session (confirmed via repeated tool-search lookups finding zero Atlassian tools).

Expected behavior

After a successful MCP handshake reporting hasTools:true, the connection should stay open long enough to list and register tools, or the reconnect-after-clear should actually succeed and retry until tools are available.

Other connectors for comparison

Other claude.ai-proxied connectors in the same account (Gmail, Google Calendar, Slack) connect and expose tools normally in the same sessions. Two other connectors (HubSpot, Figma) separately show ! Needs authentication, which is a different, expected state — only the Atlassian connector shows this connect-then-immediately-disconnect loop despite being authenticated.

Impact

The Atlassian/Jira/Confluence connector is unusable from Claude Code despite being fully authorized and reported healthy by claude mcp list.