Custom commands in .claude/commands/ not discovered after upgrading to 2.1.88

Description

After upgrading from Claude Code 2.1.87 to 2.1.88, custom commands defined as .md files in .claude/commands/ are no longer discovered or shown in /help → custom-commands.

Reproduction

1. Have a project with custom commands in .claude/commands/*.md (e.g., start.md, end.md, publish.md, etc.)
2. Confirm they work on 2.1.87 — all custom commands appear in /help custom-commands and are invocable
3. Upgrade to 2.1.88 (npm install -g @anthropic-ai/claude-code@latest)
4. Launch claude in the same project directory
5. Run /help → navigate to custom-commands tab

Expected

Custom commands from .claude/commands/ appear alongside bundled commands.

Actual

Only bundled commands appear (/batch, /claude-api, /debug, /loop, /schedule, /simplify, /update-config). No custom commands are shown or invocable.

Environment

• macOS (Darwin 24.6.0, Apple Silicon)
• Claude Code 2.1.88
• Model: Opus 4.6 (1M context), Claude Max
• Project has .claude/commands/ with 12+ custom .md command files
• .claude/settings.json present in project
• Parallel session on 2.1.87 in the same directory discovers all custom commands correctly

Workaround

Pin to 2.1.87: npm install -g @anthropic-ai/claude-code@2.1.87