[BUG/UX] Custom user command silently shadows built-in alias with no warning at creation or invocation time

Bug Description

/checkpoint is a built-in alias for /rewind. When a user creates ~/.claude/commands/checkpoint.md, the custom command silently takes over with no warning — at file creation time, at first invocation, or in /help. The user has no indication that:

• a built-in command with that name exists
• the built-in is now unreachable via the short form

This causes real confusion: I spent part of a session unsure whether /checkpoint was something I had defined or a built-in Claude Code command.

Steps to Reproduce

1. Note that /checkpoint is a built-in alias for /rewind
2. Create ~/.claude/commands/checkpoint.md (a custom skill)
3. Type /checkpoint — it now invokes the custom skill, not the built-in
4. Observe: no warning at any point (creation, invocation, or in /help)

Expected Behavior

Claude Code should warn when a custom command (user or project) has the same name as a built-in command or alias. The warning could appear:

• When the model writes the conflicting file (best: catch it early)
• At first invocation (acceptable: inform the user in the moment)
• In /help output (least disruptive, still useful)

Resolution order is a separate question — the important thing is that the conflict is surfaced rather than silently applied.

Actual Behavior

The custom command silently shadows the built-in with no indication to the user.

Environment

• Claude Code version: current
• Platform: macOS

Related

• #48750 — same class of bug on the plugin surface (/review plugin skill shadows built-in /review)