Slash commands fail to load with 'Unknown skill' error (199 commands, v2.1.89)

Bug Report

Description

All custom slash commands (from .claude/commands/) stopped being discovered by Claude Code, returning "Unknown skill" when invoked. This happened across all projects, not just one workspace.

Environment

• Claude Code version: 2.1.89 (latest at time of report)
• OS: macOS (Darwin 24.6.0)
• Number of .claude/commands/ files: 199
• All files validated: valid UTF-8, proper YAML frontmatter, no BOM, no subdirectories, no broken symlinks

Steps to Reproduce

1. Have ~199 .md files in .claude/commands/
2. Start a new Claude Code session
3. Type /challenger-review (or any custom skill)
4. Get "Unknown skill: challenger-review"

Troubleshooting Attempted

All of the following were tried with no effect:

• Restarting Claude Code (multiple times)
• Disabling all plugins
• Disabling experimental CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS env var
• Removing auto mode from settings.json
• Testing in a completely different project directory (same failure)
• Verifying file validity (frontmatter, encoding, symlinks all clean)

Resolution

The issue resolved itself after some time — possibly after a restart cycle or cache expiration. The root cause was never identified.

Expected Behavior

All valid .md files in .claude/commands/ should be discoverable as slash commands in every session.

Actual Behavior

Commands silently fail to index. No error at startup, no warning — just "Unknown skill" when trying to invoke any custom command.

Notes

• This appears to be an intermittent/transient bug — skills were working before and started working again later
• With 199 skills this could be related to scale/indexing, but the error happened across all projects (including ones with fewer commands via symlinks)
• No version change fixed it — downgrade to 2.1.88 was planned but the issue resolved before testing