[BUG] User-level custom commands in ~/.claude/commands/ not loaded into skill registry

Description

Custom slash commands (.md files) placed in ~/.claude/commands/ are not being loaded into the skill registry. The files exist on disk and have valid markdown content, but they don't appear in the available skills list and invoking them with /command-name or the Skill tool returns "Unknown skill."

These commands previously worked (as recently as 2026-02-21) and stopped appearing without any changes to the files themselves.

Environment

• Claude Code version: 2.1.47
• Platform: Windows 10 (MINGW64/Git Bash)
• Working directory: Home directory (C:\Users\<user>) — not a git repo

Steps to Reproduce

1. Place valid .md command files in ~/.claude/commands/ (e.g., my-command.md, another-command.md)
2. Start a new Claude Code session from a non-git-repo directory (home dir)
3. Check the available skills list — user-level commands are missing
4. Attempt to invoke via Skill tool — returns "Unknown skill: my-command"

What I Observed

• ls ~/.claude/commands/ shows the .md files with valid content (confirmed by reading them)
• Plugin-sourced skills (from ~/.claude/plugins/) load fine and appear in the skill registry
• Project-level commands (e.g., .claude/commands/ inside a git repo) also load fine
• Copying the files to ~/.claude/projects/<project-hash>/commands/ did not fix the issue either
• The commands worked in sessions as recently as 2026-02-21

Expected Behavior

User-level commands in ~/.claude/commands/ should be loaded into the skill registry regardless of whether the current working directory is a git repo.

Possibly Related Issues

• #18754 — "Unknown skill" errors, but that was about built-in commands
• #4646 — Custom command loading failure on Windows (old, fixed in v1.0.63)
• #19885 — Skill tool incorrectly loading commands (different behavior)