Bypass permissions mode intermittently shows permission prompts for Edit/Write

Bug Description

With bypass permissions mode toggled on (confirmed via /permissions UI), standard permission prompts intermittently appear for Edit and Write operations on normal project files.

Observed Behavior

In a single session with bypass mode active:

| Operation | File | Prompt shown? |
|-----------|------|---------------|
| Edit | cogarch.config.json | No |
| Edit | .claude/hooks/parry-wrapper.sh | No |
| Write | lessons.md | No |
| Edit | TODO.md | Yes — standard "Do you want to make this edit?" |
| Write | ~/.claude/CLAUDE.md | Yes — "Do you want to overwrite CLAUDE.md?" |

The TODO.md prompt showed the standard 3-option dialog:

1. Yes
2. Yes, allow all edits during this session (shift+tab)
3. No

This dialog should not appear in bypass mode.

The ~/.claude/CLAUDE.md overwrite prompt may be an intentional safety gate for config files — if so, documenting that distinction would help.

Environment

• Claude Code version: 2.1.71
• Platform: macOS arm64 (Darwin 25.1.0)
• Model: claude-opus-4-6
• Permission mode: bypass (toggled on via UI)

Potentially Relevant

A .claude/settings.local.json file exists with a permissions.allow array:

{
  "permissions": {
    "allow": [
      "WebSearch", "Read", "Edit", "Write",
      "Bash", "Glob", "Grep", "Agent",
      "Skill", "ToolSearch", "WebFetch(domain:github.com)"
    ]
  }
}

Per documentation, bypass mode should take precedence over allow lists. The allow list was added earlier in the session to work around a related issue (partial allow list gating tools). It's possible the presence of a permissions block in settings.local.json interacts with bypass mode in an unexpected way.

Steps to Reproduce

1. Toggle bypass permissions mode on (or launch with --dangerously-skip-permissions)
2. Have a .claude/settings.local.json with a permissions.allow array
3. Perform multiple Edit/Write operations across different project files in the same session
4. Observe that some edits go through silently while others trigger the standard permission prompt

Expected Behavior

No permission prompts should appear in bypass mode, regardless of settings.local.json content.