[Bug] Unauthorized Bash Command Execution and Update Visibility Issue

Bug Description
Two recent glitches:

1. Bash command running without a permission request. (The command was not in my permissions.allow)
2. Updates that I had approved were not displayed. (They came back after a ctrl+o, ctrl+o)

Environment Info

• Platform: darwin
• Terminal: iTerm.app
• Version: 2.0.15
• Feedback ID: e6da32da-975d-42be-9634-66b9a8ff013b

Errors

[{"error":"Error: EISDIR: illegal operation on a directory, read\n    at Module.readFileSync (node:fs:440:20)\n    at Object.readFileSync (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:9:299)\n    at FZB (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:3443:968)\n    at Object.call (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:1690:896)\n    at call.next (<anonymous>)\n    at jL (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:1690:2338)\n    at file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:3288:1328\n    at process.processTicksAndRejections (node:internal/process/task_queues:105:5)","timestamp":"2025-10-15T17:31:07.519Z"},{"error":"Error: String not found in file. Failed to apply edit.\n    at AW1 (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:542:726)\n    at yS1 (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:542:104)\n    at Object.Xo2 [as renderToolUseRejectedMessage] (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:807:3982)\n    at SlB (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:2123:4970)\n    at V$ (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:73:19415)\n    at pa (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:42814)\n    at y9 (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:38355)\n    at qm (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:38283)\n    at N$ (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:38137)\n    at KC (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:35216)","timestamp":"2025-10-15T18:09:47.226Z"},{"error":"Error: String not found in file. Failed to apply edit.\n    at AW1 (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:542:726)\n    at yS1 (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:542:104)\n    at Object.Xo2 [as renderToolUseRejectedMessage] (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:807:3982)\n    at SlB (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:2123:4970)\n    at V$ (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:73:19415)\n    at pa (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:42814)\n    at y9 (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:38355)\n    at qm (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:38283)\n    at N$ (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:38137)\n    at KC (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:35216)","timestamp":"2025-10-15T18:09:47.230Z"},{"error":"Error: String not found in file. Failed to apply edit.\n    at AW1 (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:542:726)\n    at yS1 (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:542:104)\n    at Object.Xo2 [as renderToolUseRejectedMessage] (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:807:3982)\n    at SlB (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:2123:4970)\n    at V$ (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:73:19415)\n    at pa (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:42814)\n    at y9 (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:38355)\n    at qm (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:38283)\n    at N$ (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:38137)\n    at KC (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:35216)","timestamp":"2025-10-15T18:09:47.240Z"},{"error":"Error: String not found in file. Failed to apply edit.\n    at AW1 (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:542:726)\n    at yS1 (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:542:104)\n    at Object.Xo2 [as renderToolUseRejectedMessage] (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:807:3982)\n    at SlB (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:2123:4970)\n    at V$ (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-co

Note: Error logs were truncated.