[BUG] Project commands don't take precedence over user commands as documented

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?

Project Commands Don't Take Precedence Over User Commands

When a project command (.claude/commands/*.md) and user command (~/.claude/commands/*.md) share the same name, the user command executes instead of the project command, contradicting the documented behavior.

Environment

• Claude Code Version: 2.0.76 (latest as of 2025-01-01)
• Platform: macOS (Darwin 23.6.0)
• Installation: Native

What Should Happen?

According to the official documentation:

"If a project command and user command share the same name, the project command takes precedence and the user command is silently ignored."

Actual Behavior

1. Both commands appear in autocomplete (user command should be silently ignored)
2. User command is highlighted first in autocomplete
3. User command executes when pressing Enter (project command should execute)

Error Messages/Logs

Autocomplete Output

When typing /prep, both commands appear:

/prep Load context for a new agent session (user)
/prep Load project context (project)

The user command is highlighted first by default.

Debug Logs

With claude --debug, the logs show:

Loaded 2 unique skills (managed: 0, user: 0, project: 0, legacy commands: 2)

All commands are categorized as "legacy" with no user/project distinction. This appears to be the bug. The 2 commands from ~/.claude/commands/ and .claude/commands/ are all categorized as "legacy commands" instead of being tagged as user: 1, project: 1.

Steps to Reproduce

1. Create a user command:

``bash
mkdir -p ~/.claude/commands
cat > ~/.claude/commands/prep.md << 'EOF'
---
description: Load context for a new agent session
---
# Prep (User)
This is the USER command
EOF
``

1. Create a project command with the same name:

``bash
mkdir -p .claude/commands
cat > .claude/commands/prep.md << 'EOF'
---
description: Load project context
---
# Prep (Project)
This is the PROJECT command
EOF
``

1. Start Claude Code in the project directory:

``bash
claude
``

1. Type /prep and observe autocomplete

1. Press Enter to execute

Expected: Project command executes, user command silently ignored
Actual: User command executes

Claude Model

None

Is this a regression?

No idea.

Last Working Version

_No response_

Claude Code Version

2.0.76

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

iTerm2

Additional Information

default model (currently Sonnet 4.5)