"Always allow" for directory access not persisted to settings

Description

When prompted to allow access to a directory outside the project (e.g., accessing ~/.claude from a project in ~/.dotfiles), selecting "always allow" does not persist the permission.

Expected behavior

Clicking "always allow" should add the directory to additionalDirectories in .claude/settings.json or .claude/settings.local.json.

Actual behavior

The permission is granted for the current session but not saved. The user is prompted again in future sessions.

Steps to reproduce

1. Open Claude Code in a project directory (e.g., ~/.dotfiles)
2. Perform an action that requires reading/writing to a directory outside the project (e.g., ~/.claude)
3. When prompted, select "always allow"
4. Start a new session
5. Perform the same action - you'll be prompted again

Workaround

Manually add additionalDirectories to settings:

{
  "permissions": {
    "additionalDirectories": ["~/.claude"]
  }
}

Environment

• macOS
• Claude Code (CLI)