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

[Anexria]

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.

[MuskanPaliwal]

I would like to work on this. I reproduced the behavior and traced it to ClaudeCodeAgent.UninstallHooks: after filtering Entire-managed hook entries, it separately removes Read(./.entire/metadata/**) from permissions.deny. If those are the only two settings, the file becomes {}.

There is an ownership question I would like to confirm before opening a PR. Entire adds this deny rule during hook installation, and the current tests expect uninstall to remove it. The issue proposes a narrower contract: entire agent remove claude-code should modify only hooks and leave the complete permissions object untouched, including that rule.

My proposed change is to remove the permissions cleanup from UninstallHooks and cover these cases:

• only Entire hooks: the empty settings object remains {}
• Entire hooks plus permissions: all permissions remain
• Entire hooks plus user hooks: user hooks remain
• Entire hooks plus unrelated top-level settings: those settings remain

I have reproduced the fix through the real agent add claude-code / agent remove claude-code flow and the full local CI suite passes. Does this hooks-only removal contract match the intended behavior?

[MuskanPaliwal]

I have opened draft PR #1948 with the approach described above: #1948

[Soph]

I'm trying to understand what the use case here is. Like the CLI is removing what it installs. I get the argument, that Claude should not go into those folders but if you disable entire then I'd argue more the folder should be removed? Like I feel the majority of people would want the file as it was before enabling and not just leave that rule in. And yes the rule might not have a negative impact in theory but still it feels to me not like proper cleanup and I'm having trouble seeing the exact use case.

The only thing I can see is that you want claude to with entire - but keep using entire with another agent?

[MuskanPaliwal]

That makes sense. I was treating everything outside hooks as user-owned, but Entire installs this particular deny rule too. From that perspective, removing it restores the Claude settings to their previous state.

The multi-agent case you mentioned is the one situation where keeping it could make sense: Entire stays enabled for another agent, .entire/ remains, but Claude’s hooks are removed. The issue says both Codex and Claude Code were enabled, but it doesn’t say whether that was the intended workflow.

@Anexria, could you clarify whether you wanted to keep Entire enabled for Codex while removing only the Claude integration? Also, was Read(./.entire/metadata/**) already present before you enabled Entire?