Desktop App: permission prompts still appear despite bypass permissions mode enabled

[chn893]

Description

Permission prompts ("Allow Claude to Edit [file]?") continue to appear even with all bypass permissions settings fully configured.

Environment

• Claude Desktop App (Windows)
• OS: Windows 11 Home
• App version: 2.1.87

Configuration applied (all three layers)

Desktop App Settings → Claude Code → "Allow bypass permissions mode": toggled ON

~/.claude/settings.json:
```json
{
"permissions": {
"defaultMode": "bypassPermissions",
"allow": ["Read", "Write", "Edit", "Glob", "Grep", "Bash", "Agent", ...]
},
"skipDangerousModePermissionPrompt": true
}
```

claude_desktop_config.json:
```json
{
"preferences": {
"bypassPermissionsModeEnabled": true
}
}
```

Project .claude/settings.json:
```json
{
"permissions": {
"defaultMode": "bypassPermissions"
},
"skipDangerousModePermissionPrompt": true
}
```

Steps to reproduce

1. Enable "Allow bypass permissions mode" in Desktop App settings (Claude Code tab)
2. Set defaultMode: bypassPermissions in ~/.claude/settings.json
3. Set bypassPermissionsModeEnabled: true in claude_desktop_config.json
4. Restart the Desktop App
5. Start a Claude Code session in the Code tab
6. Have Claude edit files in .claude/commands/ or .claude/memory/

Expected behavior

No permission prompts. Claude edits files uninterrupted.

Actual behavior

"Allow Claude to Edit [filepath]?" prompts appear repeatedly, requiring user action to continue. This happens on every Edit operation, even after full restart with all bypass settings configured.

Impact

Workflow is interrupted multiple times per session. The bypass permissions feature appears non-functional in the Desktop App when editing files in the .claude/ directory.

[github-actions]

Found 3 possible duplicate issues:

1. [BUG] --dangerously-skip-permissions does not bypass "edit its own settings" prompt for .claude/ directory writes #37765
2. [BUG] bypassPermissions, wildcard allow patterns, and "always allow in session" all ignored on Windows ARM (standalone app) #39348
3. [BUG] Claude Code desktop ignores permission configurations for WSL projects, requiring approval for every file operation despite proper settings #37192

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