v2.1.89 regression: Project slash commands from .claude/commands/ no longer appear

Describe the bug

After updating to v2.1.89 (latest channel), all project-level slash commands from .claude/commands/ stopped appearing in autocomplete and cannot be invoked. Typing a command name returns "Unknown skill: [name]". Downgrading to v2.1.81 (stable) immediately restores commands.

To reproduce

1. Have a project with .claude/commands/*.md files
2. Update to v2.1.89 (npm install -g @anthropic-ai/claude-code@latest)
3. Launch claude in the project directory
4. Type / followed by any command name — only built-in commands and plugin skills appear, no project commands

Expected behavior

Project commands from .claude/commands/ should appear in autocomplete and be invocable via /command_name.

Environment

• Claude Code v2.1.89 (latest channel)
• macOS Darwin 25.3.0
• Node: /usr/local/bin/node
• 56 project command files in .claude/commands/
• Plugins: compound-engineering, superpowers (issue persists with plugins disabled)

Additional context

• User-level commands (~/.claude/commands/) are also broken, not just project-level
• Even a 1-line test command file fails to appear
• claude doctor showed warnings for large CLAUDE.md (43k chars > 40k) and large MCP tools context (~27k tokens > 25k), but the issue occurs regardless of these
• The minified source shows commands are loaded with loadedFrom: "commands_DEPRECATED" — possibly related to the transition
• Workaround: npm install -g @anthropic-ai/claude-code@stable (v2.1.81)