NOAA-EMC · DavidHuber-NOAA · Feb 25, 2026 · Jan 29, 2026 · Feb 3, 2026 · Feb 4, 2026
@@ -430,215 +430,5 @@ def test_task_creation():
 3. Create modulefiles for environment setup
 4. Update environment configurations in `env/` directory
 
-## EIB MCP/RAG Server Integration (v3.6.2)
-
-The **EIB MCP-RAG Server** provides AI-assisted access to the Global Workflow system through the Model Context Protocol (MCP) with Retrieval-Augmented Generation (RAG) capabilities. This server is purpose-built to support NOAA's operational GFS, GEFS, and SFS forecasting infrastructure.
-
-### Architecture Overview
-
-```
-AI Clients (VS Code Copilot, LangFlow, Claude Desktop)
-                    │
-                    ▼ HTTP/MCP Protocol
-         ┌──────────────────────────┐
-         │  Docker MCP Gateway      │  Port 18888
-         │  (Streaming Transport)   │
-         └──────────────────────────┘
-                    │ spawns
-                    ▼
-         ┌──────────────────────────┐
-         │  MCP Server Container    │  34 tools
-         │  eib-mcp-rag:latest      │
-         └──────────────────────────┘
-                    │
-         ┌──────────┴──────────┐
-         ▼                     ▼
-    ChromaDB (8080)      Neo4j (7687)
-    Vector Embeddings    Code Graph DB
-```
-
-### Tool Categories & Separation of Concerns
-
-The MCP server implements **7 tool modules** with clear separation of concerns (SOC):
-
----
-
-#### 1. Workflow Info Tools (3 tools - Static, No DB)
-**Module**: `WorkflowInfoTools.js`
-**Purpose**: File system-based access to workflow structure - NO database dependencies
-
-| Tool | Description |
-|------|-------------|
-| `get_workflow_structure` | System architecture overview (jobs, scripts, parm, ush, sorc, env, docs) |
-| `get_system_configs` | HPC platform configurations (HERA, HERCULES, ORION, WCOSS2, GAEA) |
-| `describe_component` | File system-based component descriptions (static analysis) |
-
-**When to use**: Quick lookups, understanding directory structure, platform configs
-
----
-
-#### 2. Code Analysis Tools (4 tools - Neo4j Graph)
-**Module**: `CodeAnalysisTools.js`
-**Purpose**: Code structure analysis via graph database traversal
-
-| Tool | Description |
-|------|-------------|
-| `analyze_code_structure` | File/function/class analysis with dependency tree (depth 1-3) |
-| `find_dependencies` | Upstream imports and downstream importers (both directions) |
-| `trace_execution_path` | Call chain tracing from any function (max depth 5) |
-| `find_callers_callees` | Fan-in/fan-out analysis with complexity scoring |
-
-**When to use**: Understanding code relationships, refactoring impact, debugging call chains
-
----
-
-#### 3. Semantic Search Tools (6 tools - ChromaDB Vectors + Graph Hybrid)
-**Module**: `SemanticSearchTools.js`
-**Purpose**: RAG-powered documentation and code search
-
-| Tool | Description |
-|------|-------------|
-| `search_documentation` | Hybrid semantic + graph search across ingested docs |
-| `find_related_files` | Find files with similar import dependencies |
-| `explain_with_context` | Multi-source RAG explanations (technical, operational, config) |
-| `get_knowledge_base_status` | Vector DB + Graph DB health and statistics |
-| `list_ingested_urls` | Show all documentation sources ingested into RAG |
-| `get_ingested_urls_array` | Structured URL array for programmatic access |
-
-**When to use**: Conceptual questions, finding relevant documentation, understanding unfamiliar components
-
----
-
-#### 4. EE2 Compliance Tools (5 tools - Standards Validation)
-**Module**: `EE2ComplianceTools.js`
-**Purpose**: NOAA NWS EE2 (Enterprise Environmental 2) standards validation
-
-| Tool | Description |
-|------|-------------|
-| `search_ee2_standards` | Search EE2 compliance standards documentation |
-| `analyze_ee2_compliance` | Analyze code for EE2 compliance with recommendations |
-| `generate_compliance_report` | Generate compliance reports (summary, detailed, checklist) |
-| `scan_repository_compliance` | Full repository scan with Phase 2 SME-corrected patterns |
-| `extract_code_for_analysis` | Extract code snippets for LLM passthrough analysis |
-
-**When to use**: Pre-commit compliance checks, NCO production readiness, code reviews
-
-**Phase 2 Corrections Applied**:
-- `set -eu` is NOT required (80% false positive rate) - only `set -x` for debug logging
-- Uses `err_chk`/`err_exit` utilities instead of explicit exit statements
-- Evidence-based analysis with RST line references
-
----
-
-#### 5. Operational Tools (3 tools - HPC Procedures)
-**Module**: `OperationalTools.js`
-**Purpose**: HPC operational guidance and workflow explanations
-
-| Tool | Description |
-|------|-------------|
-| `get_operational_guidance` | Platform-specific procedures with urgency levels (routine/urgent/emergency) |
-| `explain_workflow_component` | Graph-enriched component explanations |
-| `list_job_scripts` | Categorized job script inventory (analysis, forecast, post, archive) |
-
-**When to use**: HPC deployment questions, understanding job scripts, operational procedures
-
----
-
-#### 6. GitHub Integration Tools (4 tools - Live Repository Access)
-**Module**: `GitHubTools.js`
-**Purpose**: Cross-repository analysis and issue tracking
-
-| Tool | Description |
-|------|-------------|
-| `search_issues` | Search NOAA-EMC GitHub issues (open/closed/all) |
-| `get_pull_requests` | PR information with diff context |
-| `analyze_workflow_dependencies` | Cross-repo dependency analysis (upstream/downstream/circular) |
-| `analyze_repository_structure` | Multi-repo structure comparison (global-workflow, GSI, UFS_UTILS) |
-
-**When to use**: Bug investigation, PR reviews, understanding cross-repo impacts
-
----
-
-#### 7. SDD Workflow Tools (7 tools - Development Orchestration)
-**Module**: `SDDWorkflowTools.js`
-**Purpose**: Software Design Document (SDD) framework execution
-
-| Tool | Description |
-|------|-------------|
-| `list_sdd_workflows` | List available SDD workflows |
-| `get_sdd_workflow` | Get workflow phases, steps, and metadata |
-| `execute_sdd_workflow` | Execute workflow with dry-run option |
-| `get_sdd_execution_history` | View execution history |
-| `validate_sdd_compliance` | Validate code against SDD framework |
-| `get_sdd_framework_status` | Framework integration status and metrics |
-| `execute_sdd_workflow_supervised` | Human-in-loop execution with approval gates |
-
-**When to use**: Feature development following SDD methodology, multi-step workflows
-
----
-
-#### 8. Utility Tools (2 tools - Server Management)
-**Built into**: `UnifiedMCPServer.js`
-
-| Tool | Description |
-|------|-------------|
-| `get_server_info` | MCP server info, tool counts, configuration |
-| `mcp_health_check` | Empirical health validation (heartbeat, collections, documents, queries) |
-
-**When to use**: Debugging MCP issues, verifying RAG system health
-
----
-
-### RAG Knowledge Base Sources
-
-The RAG system ingests documentation from multiple tiers:
-
-| Tier | Sources | Purpose |
-|------|---------|---------|
-| **Tier 1 Critical** | global-workflow RTD, EE2 Standards | Core workflow documentation |
-| **Tier 2 Workflow** | Rocoto, ecFlow, wxflow, PyFlow | Workflow engine documentation |
-| **Tier 3 Models** | UFS Weather Model, JEDI, FV3 | Forecast model documentation |
-| **Tier 4 Build** | Spack, spack-stack, hpc-stack | Build system documentation |
-| **Tier 5 Standards** | Google Shell Style, PEP8, NumPy docstrings | Coding standards |
-
-### When to Use MCP Tools
-
-**USE MCP tools when:**
-- Searching for concepts across documentation (semantic search)
-- Analyzing code dependencies and call chains (graph traversal)
-- Checking EE2 compliance before committing code
-- Understanding HPC platform-specific procedures
-- Investigating GitHub issues related to a component
-- Following SDD development workflows
-
-**DON'T use MCP tools when:**
-- You already have the file open and can read it directly
-- Simple file edits that don't need context research
-- The question is answered in the current conversation context
-
-### Tool Availability by Connection Mode
-
-| Mode | Available Tools | Notes |
-|------|-----------------|-------|
-| **VS Code Local** | All 34 tools | Direct stdio connection |
-| **Docker Gateway** | All 34 tools | HTTP via port 18888 |
-| **Remote (no container)** | Core workflow tools only | Use `content` parameter for file analysis |
-
-### Content Abstraction for Remote Access
-
-For remote MCP clients (e.g., LangFlow) without filesystem access, tools support content parameters:
-
-```javascript
-// Instead of filesystem path:
-analyze_ee2_compliance({ content: "#!/bin/bash\nset -x\n..." })
-
-// Batch file analysis:
-scan_repository_compliance({
-  files: [
-    { name: "JGFS_FORECAST", content: "..." },
-    { name: "exgfs_fcst.sh", content: "..." }
-  ]
-})
-```
 ---
 Remember: This is a production weather forecasting system. Changes must be thoroughly tested and should not disrupt operational workflows. Always follow the existing patterns and conventions when extending the system