Trust prompt reappears on every restart despite additionalDirectories: ["/"] set globally

Description

The folder trust prompt appears on every session start, even for directories that were previously trusted. Accepting it in one session does not persist to the next.

Environment

• Platform: macOS (Darwin 25.4.0)
• Shell: zsh
• Entrypoint: CLI

Global settings (~/.claude/settings.json)

{
  "permissions": {
    "allow": ["Read", "Write", "Edit", "Glob", "Grep", ...],
    "defaultMode": "auto",
    "additionalDirectories": ["/"]
  },
  "skipDangerousModePermissionPrompt": true,
  "skipAutoPermissionPrompt": true
}

Steps to reproduce

1. Start a Claude Code session in any directory under /Users/landon/
2. Accept the trust prompt
3. Exit the session
4. Start a new session in the same directory
5. Trust prompt appears again

Additional context

Working across many git worktree paths (e.g. /Users/landon/repos/meds-projects-worktrees/docker-mysql, /Users/landon/repos/.worktrees/25210-playwright-e2e-approval). Each unique worktree path triggers the prompt independently — and re-triggers it on restart.

Investigated ~/.claude/ thoroughly: no trust state is persisted to any file (no database, no keychain entry, no preferences file). This suggests the trust decision is held in memory only and lost on exit.

Expected: additionalDirectories: ["/"] and skipAutoPermissionPrompt: true should suppress the trust prompt globally, or trust state should persist across restarts.

Actual: Prompt reappears every session, for every path including previously-accepted ones.