[BUG] MCP proxy silently hangs on tool_use results — Claude CLI blocks waiting for complete tool_result set

Bug description

When using claude -p (headless mode) with claude.ai MCP servers, the Anthropic MCP proxy silently drops tool results. The upstream MCP server (Bear Notes) responds successfully (HTTP 200, ~44ms), but the proxy never delivers the result back to Claude CLI. Since Claude CLI requires the complete set of tool_results before continuing, this causes it to block indefinitely until the inactivity timeout fires.

Environment

• Claude CLI: 2.1.78, 2.1.79, 2.1.80
• OS: macOS 15 (Apple Silicon)
• MCP servers: claude_ai_bear (Bear Notes)
• Invocation: claude -p --output-format stream-json --allowedTools "mcp__claude_ai_bear__*"

Steps to reproduce

1. Use claude -p with claude.ai Bear Notes MCP tools enabled
2. Send a prompt that triggers multiple parallel get_note calls
3. One call returns successfully, the other never arrives from the proxy
4. Claude CLI blocks indefinitely waiting for the complete tool_result set

Consistently reproducible with specific notes — the same note always hangs through the proxy while the upstream Bear server responds normally.

Observed behavior

• Bear Notes MCP server responds HTTP 200 in ~44ms (server is healthy)
• Proxy receives the response but never forwards it to Claude CLI
• Claude CLI cannot proceed — it requires all pending tool_result messages
• Inactivity timeout eventually fires (no error, silent failure)
• Fallback retry hits the same hung call → same result
• Total pipeline timeout → failure

Key observation: This is a proxy-layer issue. The upstream server is healthy — the proxy silently drops the response.

Expected behavior

Any of:

1. Proxy delivers all results reliably
2. Per-tool timeout with a clear error message (e.g., tool_result timeout for tool_use_id X)
3. Claude CLI can continue with partial results when some tool_results are missing

Workarounds

We implemented the following workarounds in our automation pipeline:

• Track pending tool_use IDs via stream-json output to identify which call hung
• Adaptive inactivity timeout (2x when tool_use is pending)
• On MCP hang detection: fallback with restricted tools (write-only Bear tools, disabling get_note/search_notes)
• Minimum remaining timeout check before fallback attempt

Related issues

• #18745 — MCP servers failing causing Claude CLI to hang with stalled token usage
• #15945 — MCP Server causes 16+ hour hang, no timeout or stuck detection
• #36469 — Claude Code hangs indefinitely on large MCP tool responses
• #15758 — MCP tools silently disappear mid-session
• #22451 — MCP Tools hanging for 5-10 minutes then failing