Update MCP server documentation to focus on mcp-servers configuration format

[Copilot]

This PR updates the MCP (Model Context Protocol) server documentation to provide clear, streamlined guidance on MCP server configuration using the mcp-servers: format and comprehensive documentation on GitHub MCP registry integration.

Problem

The existing documentation had several issues:

• Confusing examples showing multiple configuration formats
• No clear distinction between built-in tools and MCP server configuration
• Missing documentation on MCP registry integration with gh aw mcp add
• Users were unclear about the recommended configuration approach

Solution

Updated four key documentation files to provide clear, focused guidance on the mcp-servers: configuration format:

1. MCP Integration Guide (docs/src/content/docs/guides/mcps.md)

Streamlined to show only the mcp-servers: format throughout:

mcp-servers:
  notion:
    registry: https://api.mcp.github.com/v0/servers/makenotion/notion-mcp-server
    command: npx
    args: ["-y", "@makenotion/notion-mcp-server"]
    allowed: ["search_pages", "create_page"]

Added comprehensive MCP registry integration section with gh aw mcp add command examples:

# List available MCP servers from GitHub's registry
gh aw mcp add

# Add a server to your workflow with automatic configuration
gh aw mcp add my-workflow makenotion/notion-mcp-server

2. Tools Reference (docs/src/content/docs/reference/tools.md)

Restructured to clearly separate MCP server configuration from built-in tools using the mcp-servers: format:

# Clear separation of built-in tools and MCP servers
mcp-servers:
  custom-api:
    command: "node"
    args: ["custom-mcp-server.js"]

tools:
  github:
    allowed: [create_issue, update_issue]
  playwright:
    allowed_domains: ["github.com"]

3. CLI Documentation (docs/src/content/docs/tools/cli.md)

Enhanced the MCP server management section with detailed registry features:

• Automatic configuration using the mcp-servers: format
• Registry integration with GitHub's MCP registry at https://api.mcp.github.com/v0
• Transport selection and custom tool ID support

4. Agent Instructions (.github/instructions/github-agentic-workflows.instructions.md)

Updated to show the mcp-servers: format for AI agents to understand the recommended configuration approach.

Key Benefits

Simplified Configuration: Users now have a single, clear format to learn:

• mcp-servers: - Clean top-level configuration for MCP servers
• Clear separation from built-in tools: configuration

MCP Registry Integration: Comprehensive documentation on using gh aw mcp add for easy server discovery and automatic configuration from GitHub's registry.

Streamlined User Experience: Eliminates decision fatigue and configuration confusion by focusing on a single recommended approach.

Validation: All examples compile correctly, and the mcp-servers: format generates proper lock files with registry information preserved.

This update provides a focused, streamlined approach to MCP server configuration in GitHub Agentic Workflows while maintaining all powerful features like registry integration and automatic server discovery.

Original prompt

Update documentation on mcp-servers configuration.

• review outdated documention that still uses "tools:" and nested "mcp:" fields
• differentiate "tools" vs "mcp-servers"
• discuss adding from the MCP registry

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[pelikhan]

@copilot ignore legacy or migration issues

[Copilot]

@copilot ignore legacy or migration issues

Done. I've removed all legacy format documentation and migration guidance from the MCP documentation. The docs now focus exclusively on the mcp-servers: format, eliminating confusion and providing a streamlined single-format approach. Changes committed in 6e8860c.