[Bug] Queued prompts occasionally processed without model response and missing from history

Bug Description
Sometimes Claude Code will ignore a queued prompt - the prompt displays at some point as if it were processed, but the model odesn't respond to it. Interestingly the prompt does not show up when pressing up arrow to go to previous prompts, so I think this is a harness issue rather than the model ignoring it.

Environment Info

• Platform: linux
• Terminal: vscode
• Version: 2.0.55
• Feedback ID:

Errors

[{"error":"AxiosError: timeout of 5000ms exceeded\n    at Pz.<anonymous> (file:///home/ubuntu/.local/lib/node_modules/@anthropic-ai/claude-code/cli.js:29:10448)\n    at Pz.emit (node:events:524:28)\n    at Pz.emit (node:domain:489:12)\n    at Timeout.<anonymous> (file:///home/ubuntu/.local/lib/node_modules/@anthropic-ai/claude-code/cli.js:28:3285)\n    at listOnTimeout (node:internal/timers:581:17)\n    at process.processTimers (node:internal/timers:519:7)\n    at EVA.request (file:///home/ubuntu/.local/lib/node_modules/@anthropic-ai/claude-code/cli.js:31:2130)\n    at runNextTicks (node:internal/process/task_queues:60:5)\n    at process.processTimers (node:internal/timers:516:9)\n    at async QV0 (file:///home/ubuntu/.local/lib/node_modules/@anthropic-ai/claude-code/cli.js:4249:8674)","timestamp":"2025-11-30T07:34:48.942Z"},{"error":"Error: EISDIR: illegal operation on a directory, read\n    at Module.readFileSync (node:fs:449:20)\n    at Object.readFileSync (file:///home/ubuntu/.local/lib/node_modules/@anthropic-ai/claude-code/cli.js:9:299)\n    at i22 (file:///home/ubuntu/.local/lib/node_modules/@anthropic-ai/claude-code/cli.js:4242:17034)\n    at Object.call (file:///home/ubuntu/.local/lib/node_modules/@anthropic-ai/claude-code/cli.js:1514:909)\n    at file:///home/ubuntu/.local/lib/node_modules/@anthropic-ai/claude-code/cli.js:1706:1473\n    at process.processTicksAndRejections (node:internal/process/task_queues:95:5)","timestamp":"2025-11-30T07:56:53.527Z"},{"error":"Error: EISDIR: illegal operation on a directory, read\n    at Module.readFileSync (node:fs:449:20)\n    at Object.readFileSync (file:///home/ubuntu/.local/lib/node_modules/@anthropic-ai/claude-code/cli.js:9:299)\n    at i22 (file:///home/ubuntu/.local/lib/node_modules/@anthropic-ai/claude-code/cli.js:4242:17034)\n    at Object.call (file:///home/ubuntu/.local/lib/node_modules/@anthropic-ai/claude-code/cli.js:1514:909)\n    at file:///home/ubuntu/.local/lib/node_modules/@anthropic-ai/claude-code/cli.js:1706:1473\n    at process.processTicksAndRejections (node:internal/process/task_queues:95:5)","timestamp":"2025-11-30T07:56:53.556Z"},{"error":"AxiosError: Request failed with status code 401\n    at kj (file:///home/ubuntu/.local/lib/node_modules/@anthropic-ai/claude-code/cli.js:24:1137)\n    at IncomingMessage.<anonymous> (file:///home/ubuntu/.local/lib/node_modules/@anthropic-ai/claude-code/cli.js:29:9864)\n    at IncomingMessage.emit (node:events:536:35)\n    at IncomingMessage.emit (node:domain:489:12)\n    at endReadableNT (node:internal/streams/readable:1698:12)\n    at process.processTicksAndRejections (node:internal/process/task_queues:82:21)\n    at EVA.request (file:///home/ubuntu/.local/lib/node_modules/@anthropic-ai/claude-code/cli.js:31:2130)\n    at process.processTicksAndRejections (node:internal/process/task_queues:95:5)\n    at async $T3 (file:///home/ubuntu/.local/lib/node_modules/@anthropic-ai/claude-code/cli.js:2956:460)\n    at async Promise.all (index 0)\n    at async file:///home/ubuntu/.local/lib/node_modules/@anthropic-ai/claude-code/cli.js:2942:6123","timestamp":"2025-12-02T21:03:52.897Z"}]