After head44a07ece34; Linux x64; Claude CLI2.1.303; real web dev app1280x800; Opus5.5.
Identical fault: real CLI wrapper drops only mcp_set_servers requests.
Baseline: OK. Two messages failed after two90s registration timeouts each.
Fault removed. /compact showed Context compacted70.8K ->1.44K tokens. Next normal message returned OK.
Baseline native ID: 4deb6845-f81a-48fe-8e99-ebe0fde44e97
Observed logs:
[21:45:11.528] WARN (#7912): orchestration-v2.claude-mcp-registration-timeout

  {

    threadId: 'e87ddbb9-040e-4b3a-b009-201b9711b273',

    providerSessionId: 'provider-session:provider-instance:claudeAgent:thread:e87ddbb9-040e-4b3a-b009-201b9711b273:c6fa124d-760a-4197-8ccf-938f0c067365'

  }

(node:1564082) [CLAUDE_SDK_CAN_USE_TOOL_SHADOWED] Warning: canUseTool will not be invoked: permissionMode 'bypassPermissions' auto-approves every tool call (except explicit deny rules) before the callback is consulted. To gate every tool call, use a PreToolUse hook instead.

[21:45:12.583] INFO (#9044) http.span=64ms: Sent HTTP response

  http.method: POST

[21:46:41.567] WARN (#7912): orchestration-v2.claude-mcp-registration-timeout

  {

    threadId: 'e87ddbb9-040e-4b3a-b009-201b9711b273',

    providerSessionId: 'provider-session:provider-instance:claudeAgent:thread:e87ddbb9-040e-4b3a-b009-201b9711b273:c6fa124d-760a-4197-8ccf-938f0c067365'

  }

[21:46:41.592] ERROR (#7912): orchestration V2 provider turn start failed

  {

    runId: 'run:thread:e87ddbb9-040e-4b3a-b009-201b9711b273:ordinal:2',

[21:48:30.777] WARN (#10222): orchestration-v2.claude-mcp-registration-timeout

  {

    threadId: 'e87ddbb9-040e-4b3a-b009-201b9711b273',

    providerSessionId: 'provider-session:provider-instance:claudeAgent:thread:e87ddbb9-040e-4b3a-b009-201b9711b273:c6fa124d-760a-4197-8ccf-938f0c067365'

  }

(node:1564082) [CLAUDE_SDK_CAN_USE_TOOL_SHADOWED] Warning: canUseTool will not be invoked: permissionMode 'bypassPermissions' auto-approves every tool call (except explicit deny rules) before the callback is consulted. To gate every tool call, use a PreToolUse hook instead.

[21:48:30.841] WARN (#11505): Could not stop an exited agent's scope

  { unit: 't3code-claude-e80e213a.scope', exitCode: 5 }

[21:50:00.805] WARN (#10222): orchestration-v2.claude-mcp-registration-timeout

  {

    threadId: 'e87ddbb9-040e-4b3a-b009-201b9711b273',

    providerSessionId: 'provider-session:provider-instance:claudeAgent:thread:e87ddbb9-040e-4b3a-b009-201b9711b273:c6fa124d-760a-4197-8ccf-938f0c067365'

  }

[21:50:00.832] ERROR (#10222): orchestration V2 provider turn start failed

  {

    runId: 'run:thread:e87ddbb9-040e-4b3a-b009-201b9711b273:ordinal:3',

uncertain_history_delivery log count: 0
runs
{"ordinal": 1, "status": "completed"}
{"ordinal": 2, "status": "failed"}
{"ordinal": 3, "status": "failed"}
{"ordinal": 4, "status": "completed"}
{"ordinal": 5, "status": "completed"}
provider_threads
{"nativeThreadRef": {"driver": "claudeAgent", "nativeId": "4deb6845-f81a-48fe-8e99-ebe0fde44e97", "strength": "strong"}, "status": "idle"}
context_handoffs
{"strategy": "delta_since_target_last_seen", "status": "ready", "delivery": {"nativeThreadId": "4deb6845-f81a-48fe-8e99-ebe0fde44e97", "status": "inline"}}
{"strategy": "delta_since_target_last_seen", "status": "ready", "delivery": {"nativeThreadId": "4deb6845-f81a-48fe-8e99-ebe0fde44e97", "status": "inline"}}