Claude Code Markdown Multi-line Agents Not Getting Detected

# Summary
Claude Code has a critical bug where several users are reporting that the cloud code is not detecting their custom agents.

In my case it was affecting not only the agents but the commands as well.

Looks like the root cause is a system tool problem (RIPGREP), a new format for agents on the .yml, and an issue related to multi-line .md files for agents and commands:

https://github.com/anthropics/claude-code/issues/4623#issuecomment-3187221181

# Environment
Platform: Dev Container - Windows
Claude Code: Any version, tested until 1.0.61
Claude-Flow: 2.0.0-alpha.89

# Steps to reproduce
1. Fresh installation
1. npx claude-code@alpha init --force
1. claude -> /agents

# Solution
For me, what worked was to **move agents and commands from the subfolders** and put them in the .claude/agents folder directly. I'm on the Claude Code version 1.0.76 and didn't try this fix on the latest version