[BUG] Slash commands appear duplicated in /help output with one set marked "(project)"

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 /help, custom slash commands from ~/.claude/commands/ appear twice in
the output, with one set marked "(project)" even though there is no project-level
.claude directory.

Environment:

• Claude Code version: 2.025
• OS: macOS (Darwin 24.5.0)
• Working directory: ~/1brutus (not a project with .claude/)
• User-level config: ~/.claude/ (git clone of custom config repo)

Configuration:

• User-level config at: ~/.claude/
• 6 slash commands in ~/.claude/commands/ (arch.md, dbg.md, pe.md, swe.md,

test-health.md, tl.md)

• 2 hooks in ~/.claude/hooks/ (pre_safety_check.sh, post_telemetry.sh)
• settings.json with hooks configuration
• agents/ and skills/ directories with documentation
• Project-level config: None (no .claude/ directory in ~/1brutus)

Each command appears exactly twice, with one set labeled "(project)":

❯ /arch Software Architect agent for feature integration planning
❯ /arch Software Architect agent for feature integration planning
/dbg Code Debugger agent for troubleshooting runtime errors and
/dbg Code Debugger agent for troubleshooting runtime errors and
/pe Production Engineering agent for infrastructure operations
/pe Production Engineering agent for infrastructure operations
/swe Software Engineering agent for feature implementation with
/swe Software Engineering agent for feature implementation with
/test-health Generate test health report with flaky and slow test
↓ /test-health Generate test health report with flaky and slow test
analysis (project)

Additional context:

• The commands themselves work correctly despite appearing twice
• The "(project)" label appears to be incorrect - there is no project-level config
• Previously had some .md files in hooks/ directory (removed) and settings.json

was missing (now added), but duplicates persist after fixing these issues

• Config repo: https://github.com/acartine/osterman

Verification performed:
# Confirmed only one source of commands
ls ~/.claude/commands/
# arch.md dbg.md pe.md swe.md test-health.md tl.md

# Confirmed no project-level config
ls .claude/
# ls: .claude/: No such file or directory

# Confirmed no obsolete hook .md files
ls ~/.claude/hooks/
# post_telemetry.sh pre_safety_check.sh

What Should Happen?

Each slash command should appear once in /help output.

Error Messages/Logs

Steps to Reproduce

1. Clone custom .claude config to ~/.claude/ (e.g., git clone

https://github.com/acartine/osterman.git ~/.claude)

1. Work in a project directory with no project-level .claude/ (e.g., cd ~/1brutus)
2. Start Claude Code
3. Run /help

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.025

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

iTerm2

Additional Information

<img width="603" height="445" alt="Image" src="https://github.com/user-attachments/assets/35677f72-47af-40fa-a82c-1e6c903dd94c" />

https://github.com/acartine/osterman.git (to reproduce user level .claude state)