agent remove claude-code deletes unrelated .claude/settings.json keys

Summary

entire agent remove claude-code removes unrelated keys from the repository's .claude/settings.json instead of removing only Entire-managed Claude hooks.

Environment

• Entire CLI: 0.9.0
• OS: Windows amd64
• Repository already enabled for both Codex and Claude Code

Reproduction

Start with a project-level .claude/settings.json containing Entire-managed hooks plus an unrelated permission:

{
  "hooks": {
    "SessionStart": [
      {
        "matcher": "",
        "hooks": [
          {
            "type": "command",
            "command": "entire hooks claude-code session-start"
          }
        ]
      }
    ]
  },
  "permissions": {
    "deny": [
      "Read(./.entire/metadata/**)"
    ]
  }
}

Run:

entire agent remove claude-code

CLI output:

Removed Claude Code hooks.

Actual resulting file:

{}

The unrelated permissions.deny setting is removed together with the Entire hooks.

Expected Behavior

Only Entire-managed Claude Code hook entries should be removed. Unrelated top-level keys and unrelated hook entries should be preserved.

For the example above, the resulting file should be:

{
  "permissions": {
    "deny": [
      "Read(./.entire/metadata/**)"
    ]
  }
}

Workaround

Inspect the diff immediately after agent removal and manually restore unrelated Claude settings.

Acceptance Criteria

• entire agent remove claude-code removes only Entire-owned hooks.
• Unrelated .claude/settings.json keys survive unchanged.
• A regression test covers mixed Entire and non-Entire Claude settings.

Start with the entire agent remove claude-code command and its handling of .claude/settings.json; reproduce the issue using the mixed settings example in this report. Add a regression test covering Entire and unrelated Claude settings, then verify that removal preserves unrelated top-level keys and hook entries.