Current main dd5b5401e1; Linux x64; Claude CLI 2.1.303; web client 1280x800.
Baseline: Opus 5.5 replied OK.
Fault injection: real CLI stdin wrapper drops only mcp_set_servers control requests.
Two normal messages each hit two 90-second registration timeouts.
After removing fault, /compact created replacement native session.
Observed logs:
[21:28:21.248] WARN (#7948): orchestration-v2.claude-mcp-registration-timeout

  {

    threadId: 'thread:project:b47b8805-d2cc-4f51-8732-df96d513098d:0ce22817-33ff-4513-8ff7-15e9ff79ef77',

    providerSessionId: 'provider-session:provider-instance:claudeAgent:thread:thread%3Aproject%3Ab47b8805-d2cc-4f51-8732-df96d513098d%3A0ce22817-33ff-4513-8ff7-15e9ff79ef77:c7c193d7-227a-43b1-ae94-b1b27fcf39e2'

  }

(node:1538926) [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.

[21:28:21.612] INFO (#8962) http.span=33ms: Sent HTTP response

  http.method: POST

[21:29:51.296] WARN (#7948): orchestration-v2.claude-mcp-registration-timeout

  {

    threadId: 'thread:project:b47b8805-d2cc-4f51-8732-df96d513098d:0ce22817-33ff-4513-8ff7-15e9ff79ef77',

    providerSessionId: 'provider-session:provider-instance:claudeAgent:thread:thread%3Aproject%3Ab47b8805-d2cc-4f51-8732-df96d513098d%3A0ce22817-33ff-4513-8ff7-15e9ff79ef77:c7c193d7-227a-43b1-ae94-b1b27fcf39e2'

  }

[21:29:51.324] ERROR (#7948): orchestration V2 provider turn start failed

  {

    runId: 'run:thread:thread%3Aproject%3Ab47b8805-d2cc-4f51-8732-df96d513098d%3A0ce22817-33ff-4513-8ff7-15e9ff79ef77:ordinal:2',

[21:31:45.074] WARN (#9976): orchestration-v2.claude-mcp-registration-timeout

  {

    threadId: 'thread:project:b47b8805-d2cc-4f51-8732-df96d513098d:0ce22817-33ff-4513-8ff7-15e9ff79ef77',

    providerSessionId: 'provider-session:provider-instance:claudeAgent:thread:thread%3Aproject%3Ab47b8805-d2cc-4f51-8732-df96d513098d%3A0ce22817-33ff-4513-8ff7-15e9ff79ef77:c7c193d7-227a-43b1-ae94-b1b27fcf39e2'

  }

(node:1538926) [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.

[21:31:45.652] INFO (#11099) http.span=20ms: Sent HTTP response

  http.method: POST

[21:33:15.105] WARN (#9976): orchestration-v2.claude-mcp-registration-timeout

  {

    threadId: 'thread:project:b47b8805-d2cc-4f51-8732-df96d513098d:0ce22817-33ff-4513-8ff7-15e9ff79ef77',

    providerSessionId: 'provider-session:provider-instance:claudeAgent:thread:thread%3Aproject%3Ab47b8805-d2cc-4f51-8732-df96d513098d%3A0ce22817-33ff-4513-8ff7-15e9ff79ef77:c7c193d7-227a-43b1-ae94-b1b27fcf39e2'

  }

[21:33:15.126] ERROR (#9976): orchestration V2 provider turn start failed

  {

    runId: 'run:thread:thread%3Aproject%3Ab47b8805-d2cc-4f51-8732-df96d513098d%3A0ce22817-33ff-4513-8ff7-15e9ff79ef77:ordinal:3',

[21:33:45.315] WARN (#12186): Provider resume failed; attempting a fresh native session

  {

    driver: 'claudeAgent',

    providerThreadId: 'provider-thread:provider:claudeAgent:native-thread:pending%3Arun%3Athread%3Athread%253Aproject%253Ab47b8805-d2cc-4f51-8732-df96d513098d%253A0ce22817-33ff-4513-8ff7-15e9ff79ef77%3Aordinal%3A1',

    runId: 'run:thread:thread%3Aproject%3Ab47b8805-d2cc-4f51-8732-df96d513098d%3A0ce22817-33ff-4513-8ff7-15e9ff79ef77:ordinal:4',

    reason: 'uncertain_history_delivery',

    errorTag: 'ProviderAdapterTurnStartError'

  }

runs
{"ordinal": 1, "status": "completed"}
{"ordinal": 2, "status": "failed"}
{"ordinal": 3, "status": "failed"}
{"ordinal": 4, "status": "completed"}
provider_threads
{"nativeThreadRef": {"driver": "claudeAgent", "nativeId": "d560e93f-ef3c-4d09-9be7-6107278e72ae", "strength": "strong"}, "status": "idle"}
context_handoffs
{"strategy": "delta_since_target_last_seen", "status": "ready", "delivery": {"nativeThreadId": "8f189dfe-59c4-4b6a-a287-aa38a5f2e0a1", "status": "pending"}}
{"strategy": "full_thread_summary", "status": "ready"}