Project-level .claude/commands/ files not loaded into skills list

Description

Project-level .claude/commands/*.md files are not appearing in the skills list at session start, while global ~/.claude/commands/*.md files do load correctly.

Steps to Reproduce

1. Place command files in both ~/.claude/commands/ (global) and .claude/commands/ (project)
2. Have some commands that exist only at project level (not in global)
3. Start a new Claude Code session in the project
4. Check the available skills list in the system-reminder

Observed Behavior

• Global ~/.claude/commands/*.md files: appear in skills list
• Project .claude/commands/*.md files that also exist in global: appear (via global copy)
• Project .claude/commands/*.md files that only exist at project level: NOT in skills list

The commands can still be executed via other means (e.g., shell reap run <command>), but they cannot be invoked via the Skill tool because they are absent from the skills list.

Expected Behavior

Project-level .claude/commands/*.md files should appear in the skills list, consistent with backward compatibility for the commands format. The docs state that files in .claude/commands/ still work and support the same frontmatter as .claude/skills/.

Environment

• OS: macOS (Darwin 23.1.0)
• Node: v22.22.0
• Tool using .claude/commands/: REAP (v0.13.4), which intentionally installs commands only at project level to avoid polluting skills in unrelated projects