[Bug] Claude Code resumes autonomously after pause command instead of waiting for explicit user resume

<img width="1167" height="662" alt="Image" src="https://github.com/user-attachments/assets/83924927-2ed5-4cfb-baf7-8b8a5c69bd8d" />

Bug Description
I told claude to pause what it was doing and "resume in earnest in 2 hours" before going to bed. when i got back to my desk I see "checking in. ." with a list of questions wondering if i'd like to resume now or later, etc. just waiting for my response. UNACCEPTABLE. a wasted night. [Image #4]

Environment Info

• Platform: win32
• Terminal: WarpTerminal
• Version: 2.1.117
• Feedback ID: 022edb93-df90-44f0-bde1-288fcb8d5d74

Errors

[{"error":"Error: ENOTDIR: not a directory, mkdir 'G:'\n    at async mkdir (B:/~BUN/root/src/entrypoints/cli.js:53:655)\n    at async call (B:/~BUN/root/src/entrypoints/cli.js:3247:512)\n    at async Q91 (B:/~BUN/root/src/entrypoints/cli.js:4247:8751)","timestamp":"2026-05-01T12:15:42.781Z"},{"error":"MaxFileReadTokenExceededError: File content (25178 tokens) exceeds maximum allowed tokens (25000). Use offset and limit parameters to read specific portions of the file, or search for specific content instead of reading the whole file.\n    at BL_ (B:/~BUN/root/src/entrypoints/cli.js:4788:12679)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-05-01T13:15:11.678Z"},{"error":"MaxFileReadTokenExceededError: File content (33270 tokens) exceeds maximum allowed tokens (25000). Use offset and limit parameters to read specific portions of the file, or search for specific content instead of reading the whole file.\n    at BL_ (B:/~BUN/root/src/entrypoints/cli.js:4788:12679)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-05-01T13:15:31.465Z"},{"error":"MaxFileReadTokenExceededError: File content (40211 tokens) exceeds maximum allowed tokens (25000). Use offset and limit parameters to read specific portions of the file, or search for specific content instead of reading the whole file.\n    at BL_ (B:/~BUN/root/src/entrypoints/cli.js:4788:12679)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-05-01T13:15:32.146Z"},{"error":"Error: File does not exist. Note: your current working directory is G:\\My Drive\\Projects Merge\\ObsidianNexus.\n    at call (B:/~BUN/root/src/entrypoints/cli.js:4797:7634)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-05-01T13:17:34.084Z"},{"error":"Error: 429 {\"type\":\"error\",\"error\":{\"type\":\"rate_limit_error\",\"message\":\"This request would exceed your account's rate limit. Please try again later.\"},\"request_id\":\"req_011Cac8tjchbjQzcL1yWQtTA\"}\n    at generate (B:/~BUN/root/src/entrypoints/cli.js:11:54279)\n    at makeRequest (B:/~BUN/root/src/entrypoints/cli.js:50:4943)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-05-01T16:06:23.246Z"},{"error":"Error: Could not resolve authentication method. Expected either apiKey or authToken to be set. Or for one of the \"X-Api-Key\" or \"Authorization\" headers to be explicitly omitted\n    at validateHeaders (B:/~BUN/root/src/entrypoints/cli.js:50:1013)\n    at buildHeaders (B:/~BUN/root/src/entrypoints/cli.js:50:8079)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-05-01T16:20:32.551Z"},{"error":"Error: Could not resolve authentication method. Expected either apiKey or authToken to be set. Or for one of the \"X-Api-Key\" or \"Authorization\" headers to be explicitly omitted\n    at validateHeaders (B:/~BUN/root/src/entrypoints/cli.js:50:1013)\n    at buildHeaders (B:/~BUN/root/src/entrypoints/cli.js:50:8079)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-05-01T16:20:37.189Z"},{"error":"Error: File does not exist. Note: your current working directory is G:\\My Drive\\Projects Merge\\ObsidianNexus.\n    at call (B:/~BUN/root/src/entrypoints/cli.js:4797:7634)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-05-01T17:02:48.059Z"},{"error":"MaxFileReadTokenExceededError: File content (43693 tokens) exceeds maximum allowed tokens (25000). Use offset and limit parameters to read specific portions of the file, or search for specific content instead of reading the whole file.\n    at BL_ (B:/~BUN/root/src/entrypoints/cli.js:4788:12679)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-05-01T17:56:18.944Z"},{"error":"Error: File does not exist. Note: your current working directory is G:\\My Drive\\Projects Merge\\ObsidianNexus.\n    at call (B:/~BUN/root/src/entrypoints/cli.js:4797:7634)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-05-01T17:56:19.229Z"},{"error":"Error\n    at generate (B:/~BUN/root/src/entrypoints/cli.js:11:54094)\n    at makeRequest (B:/~BUN/root/src/entrypoints/cli.js:50:4943)\n    at processTicksAndRejections (unknown:7:39)","timestamp":"2026-05-01T17:59:18.891Z"},{"error":"Error: 401 {\"type\":\"error\",\"error\":{\"type\":\"authentication_error\",\"message\":\"OAuth authentication is…

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