"Allow from this project" permission prompt doesn't persist to project settings.json

Bug Description

When prompted for tool permissions (e.g., "Do you want to proceed?" for Read/Edit/Write access), selecting option 2 "Yes, allow reading from X from this project" does not persist the permission to the project settings file.

Expected Behavior

Selecting "Yes, allow [action] from [path] from this project" should write the permission rule to ~/.claude/projects/<project-path>/settings.json so the user is not prompted again.

Actual Behavior

The permission is never saved. The user is prompted repeatedly for the same paths across sessions — including the project's own working directory.

Steps to Reproduce

1. Start Claude Code in a project directory
2. Trigger any tool that reads a file (e.g., cat ~/.claude/settings.json)
3. When prompted, select option 2: "Yes, allow reading from .claude/ from this project"
4. Start a new session in the same project
5. Trigger the same tool — you are prompted again
6. Inspect ~/.claude/projects/<project-path>/settings.json — the permission was never written

Additional Details

• Even after manually creating the settings.json file with correct structure and permissions, Claude Code still does not append new "allow from this project" selections to it
• The file exists and is readable/writable
• Manually added permissions in the file DO work — they are respected and suppress prompts
• Only the interactive "allow from this project" save path is broken

Environment

• macOS (Darwin 25.3.0)
• Claude Code CLI