Update of GitHub Copilot Instructions file for current MCP/RAG system

[TerrenceMcGuinness-NOAA]

Update Copilot Instructions with MCP/RAG Server Integration

Summary

This PR updates the .github/copilot-instructions.md file to provide comprehensive documentation for the EIB MCP-RAG Server integration (v3.6.2), which provides AI-assisted access to the Global Workflow system through the Model Context Protocol (MCP) with Retrieval-Augmented Generation (RAG) capabilities.

Changes

1. Reorganized Document Structure

• Moved "Essential Developer Workflows" section (build commands, experiment setup, platform-specific development) to follow the "Workflow Directory Structure" section
• This places build/setup instructions after developers understand the directory layout they'll be working with

2. Added Complete MCP/RAG Server Documentation

Architecture Overview

• Added architecture diagram showing the Docker MCP Gateway flow
• Documented the dual-database system: ChromaDB (vector embeddings) + Neo4j (code graph)
• Specified gateway port (18888) and protocol version (2025-06-18)

Tool Categories with Separation of Concerns (SOC)

Documented all 34 tools across 7 modules:

Module	Tools	Purpose
Workflow Info Tools	3	Static filesystem queries (no DB)
Code Analysis Tools	4	Neo4j graph-based code analysis
Semantic Search Tools	6	ChromaDB + Neo4j hybrid RAG search
EE2 Compliance Tools	5	NCO production standards validation
Operational Tools	3	HPC procedures and job scripts
GitHub Integration Tools	4	Cross-repo analysis and issue tracking
SDD Workflow Tools	7	Development workflow orchestration
Utility Tools	2	Server health and management

RAG Knowledge Base Sources

Documented the 5-tier documentation ingestion hierarchy:

• Tier 1: Critical (global-workflow, UFS-Utils, EE2 Standards)
• Tier 2: Workflow engines (Rocoto, ecFlow, wxflow, PyFlow)
• Tier 3: Models (UFS Weather Model, JEDI, FV3)
• Tier 4: Build systems (Spack, spack-stack, hpc-stack)
• Tier 5: Coding standards (Google Shell Style, PEP8, NumPy)

Usage Guidelines

• Added "When to Use MCP Tools" guidance
• Documented tool availability by connection mode (VS Code Local, Docker Gateway, Remote)
• Added Content Abstraction patterns for remote MCP clients

3. Removed Outdated Information

• Replaced obsolete tool names and descriptions
• Removed references to deprecated server locations
• Updated from placeholder tool descriptions to actual implemented tools

Testing

• Verified all tool names match actual MCP server implementation
• Confirmed architecture diagram matches current deployment
• Validated tool counts against UnifiedMCPServer.js registration

Related Issues

• Supports MCP/RAG development for AI-assisted Global Workflow operations
• Enables external users to leverage MCP tools via Docker Gateway

Reviewers

Please verify:

1. Tool descriptions accurately reflect current functionality
2. Architecture diagram matches production deployment
3. EE2 Compliance section correctly documents Phase 2 SME corrections

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Note: This update aligns the copilot-instructions.md with the EIB MCP-RAG Server v3.6.2 codebase surveyed on December 31, 2025.

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[DavidHuber-NOAA]

Thanks for the added context @TerrenceMcGuinness-NOAA!

[DavidHuber-NOAA]

Sorry, spoke too soon. I do have a few documentation suggestions.