[Bug] Tool permissions silently denied without user prompt despite allow-list configuration

Bug Description
Tool permissions configured as allowed are silently denied without prompting the user. The user is never shown a permission
dialog -- Claude receives a "Permission denied" error and cannot retry.

Affected tools: gh CLI commands (gh issue create, gh pr comment), rm on temp files, and general Bash commands that were
previously approved in the same session or configured as always-allowed in CLAUDE.md.

Expected behavior: Either execute the command (if in the allow list) or prompt the user to approve/deny.

Actual behavior: Command is silently denied. User sees Claude reporting "Permission denied" but is never shown a prompt. This
forces the user to manually run commands that Claude should be handling.

Frequency: Intermittent but recurring across multiple sessions over several days (2026-02-08 through 2026-02-10). Same commands
succeed sometimes and fail other times within the same conversation.

Environment: macOS Darwin 25.2.0 arm64, Claude Code CLI with Opus 4.6.

Note: gh pr commands are explicitly listed as always-allowed in the project CLAUDE.md under Tool Usage Policy. rm on temp files
containing pulled secrets was denied even though other rm commands succeeded earlier in the session.

Environment Info

• Platform: darwin
• Terminal: windsurf
• Version: 2.1.37
• Feedback ID: 379b4f9d-ee3a-40b3-afb5-60c3fbb41b9a

Errors

[{"error":"Error: ENOENT: no such file or directory, open '/Users/quentin/.claude/remote-settings.json'\n    at openSync (unknown)\n    at <anonymous> (/$bunfs/root/claude:12:947)\n    at oC (/$bunfs/root/claude:11:49132)\n    at readSync (/$bunfs/root/claude:12:875)\n    at tC (/$bunfs/root/claude:6113:113)\n    at TC (/$bunfs/root/claude:6115:226)\n    at BAA (/$bunfs/root/claude:178:8143)\n    at xBR (/$bunfs/root/claude:178:8306)\n    at gKD (/$bunfs/root/claude:179:1202)\n    at zAT (/$bunfs/root/claude:179:2080)","timestamp":"2026-02-09T22:02:39.609Z"},{"error":"Error: NON-FATAL: Lock acquisition failed for /Users/quentin/.local/share/claude/versions/2.1.37 (expected in multi-process scenarios)\n    at GFR (/$bunfs/root/claude:3584:2098)\n    at ebA (/$bunfs/root/claude:3584:1209)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-02-09T22:02:39.765Z"},{"error":"MaxFileReadTokenExceededError: File content (26886 tokens) exceeds maximum allowed tokens (25000). Please use offset and limit parameters to read specific portions of the file, or use the GrepTool to search for specific content.\n    at izB (/$bunfs/root/claude:3260:3309)\n    at async call (/$bunfs/root/claude:3269:2420)\n    at async <anonymous> (/$bunfs/root/claude:5778:1675)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-02-10T13:26:02.986Z"},{"error":"Error: EISDIR: illegal operation on a directory, read\n    at readFileSync (unknown)\n    at <anonymous> (/$bunfs/root/claude:12:742)\n    at oC (/$bunfs/root/claude:11:49132)\n    at readFileSync (/$bunfs/root/claude:12:701)\n    at nzB (/$bunfs/root/claude:6110:17996)\n    at call (/$bunfs/root/claude:3269:2360)\n    at yO8 (/$bunfs/root/claude:3447:13995)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-02-10T15:01:14.579Z"}]