[BUG] User Agents Incorrectly Marked as "Overridden by projectSettings"

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Description

When running /agents, user-level agents are incorrectly displayed with a warning indicator ⚠ overridden by projectSettings, even though the project has no agent configuration.

Actual Behavior

User agents display with the ⚠ overridden by projectSettings warning, suggesting there's a project-level override when none exists.

Environment

• The project's .claude/settings.json contains:

``json
{
"permissions": {
"deny": [
"Read(./.idea/**)",
"Read(./dist/**)",
...
]
}
}
``

• No agent configuration exists in the project
• User-level agents are present in ~/.claude/agents/

Output Example

User agents (/Users/.../.claude/agents)
  code-review · sonnet ⚠ overridden by projectSettings
  code-auditor · sonnet ⚠ overridden by projectSettings
  backend-ts · sonnet ⚠ overridden by projectSettings

Project agents (/Users/.../.claude/agents)
  code-review · sonnet
  code-auditor · sonnet
  backend-ts · sonnet

What Should Happen?

User agents should not show the "overridden by projectSettings" warning when the project settings do not contain any agent configuration.

Error Messages/Logs

Steps to Reproduce

1. Create a project with a .claude/settings.json that contains only permissions (no agent configuration)
2. Have user-level agents defined in ~/.claude/agents/
3. Run /agents command in the project

Claude Model

Other

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.0.24 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Other

Additional Information

Model: Haiku
Terminal/Shell: WebStorm terminal