[BUG] Trust dialog acceptance not persisted to .claude.json

Bug Description

The "trust this directory" dialog acceptance is not being persisted to ~/.claude.json. The hasTrustDialogAccepted field remains false even after accepting the dialog, causing the trust prompt to reappear on every session start for affected directories.

Evidence

Inspecting ~/.claude.json shows that projectOnboardingSeenCount increments correctly (reached 39 for one directory), proving the file is being written to — but hasTrustDialogAccepted stays false. This means the counter write succeeds but the trust flag write does not.

Example from ~/.claude.json:

{
  "/Users/<user>": {
    "hasTrustDialogAccepted": false,
    "projectOnboardingSeenCount": 39,
    "hasCompletedProjectOnboarding": true
  }
}

In this case, 3 out of 19 project directories had the issue (the home directory and 2 project directories). The remaining 16 had hasTrustDialogAccepted: true.

Steps to Reproduce

1. Open Claude Code in a directory (home directory in my case)
2. Accept the trust dialog when prompted
3. Close the session
4. Inspect ~/.claude.json — hasTrustDialogAccepted is false for the affected project entry
5. Open Claude Code again in the same directory — trust dialog reappears

Not 100% reproducible — only affects some directories, not all. Unclear what differentiates the affected ones.

Workaround

Manually setting hasTrustDialogAccepted: true in ~/.claude.json via a script, or using a SessionStart hook to auto-set the flag.

Environment

• Claude Code version: 2.1.80
• OS: macOS 15.6.1 (Darwin 24.6.0)
• Shell: zsh