Initial commit: RAG MCP Server with relationship graph

Features:
- Vector search with Pinecone + Vertex AI embeddings
- Document relationships (link, unlink, related, graph)
- Auto-link with LLM analysis
- Intelligent merge with Gemini

Modular structure:
- clients/: Pinecone, Vertex AI
- tools/: core, relations, stats
- utils/: validation, logging

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

deploy.sh

@@ -0,0 +1,33 @@
+#!/bin/bash
+# RAG MCP Server Deploy Script
+
+HOST="root@10.253.100.107"
+REMOTE_DIR="/root/rag-mcp"
+SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
+
+echo "📦 Copying project files to rag-mcp..."
+
+# Create directories
+ssh ${HOST} "mkdir -p ${REMOTE_DIR}/{clients,tools,utils}"
+
+# Copy files
+scp "${SCRIPT_DIR}/server.py" "${SCRIPT_DIR}/config.py" "${SCRIPT_DIR}/pyproject.toml" ${HOST}:${REMOTE_DIR}/
+scp "${SCRIPT_DIR}/clients/"*.py ${HOST}:${REMOTE_DIR}/clients/
+scp "${SCRIPT_DIR}/tools/"*.py ${HOST}:${REMOTE_DIR}/tools/
+scp "${SCRIPT_DIR}/utils/"*.py ${HOST}:${REMOTE_DIR}/utils/
+
+echo "🔄 Restarting service..."
+ssh ${HOST} << 'EOF'
+cd /root/rag-mcp
+PID=$(pgrep -f "uv run.*server.py" | head -1)
+if [ -n "$PID" ]; then
+    kill $PID 2>/dev/null
+    sleep 2
+fi
+setsid uv run --with fastmcp --with pinecone --with python-dotenv --with requests python server.py </dev/null >/tmp/rag-mcp.log 2>&1 &
+sleep 3
+ps aux | grep "server.py" | grep -v grep && echo "✅ Service started" || echo "⚠️ Service not running"
+echo ""
+echo "📋 Recent logs:"
+tail -15 /tmp/rag-mcp.log 2>/dev/null || echo "No logs yet"
+EOF