Clean and organize project structure

Major reorganization:
- Created scripts/ directory for all utility scripts
- Created config/ directory for configuration files
- Moved all test files to tests/ directory
- Updated all script paths to work with new structure
- Updated README.md with new project structure diagram

New structure:
├── src/          # Source code (API + MCP)
├── scripts/      # Utility scripts (start-*.sh, docs_server.py, etc.)
├── tests/        # All test files and debug utilities
├── config/       # Configuration files (JSON, Caddy config)
├── docs/         # Documentation website
└── logs/         # Log files

All scripts updated to use relative paths from project root.
Documentation updated with new folder structure.

🤖 Generated with [Claude Code](https://claude.ai/code)

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

tests/check_neo4j_data.py

@@ -0,0 +1,90 @@
+#!/usr/bin/env python3
+"""
+Check what data is stored in Neo4j
+"""
+
+import asyncio
+from neo4j import AsyncGraphDatabase
+import json
+
+# Configuration
+NEO4J_URL = "bolt://localhost:7687"
+NEO4J_USER = "neo4j"
+NEO4J_PASSWORD = "langmem_neo4j_password"
+
+async def check_neo4j_data():
+    """Check Neo4j data stored by LangMem"""
+    print("🔍 Checking Neo4j Data from LangMem")
+    print("=" * 50)
+    
+    try:
+        driver = AsyncGraphDatabase.driver(NEO4J_URL, auth=(NEO4J_USER, NEO4J_PASSWORD))
+        
+        async with driver.session() as session:
+            # Check all nodes
+            print("1. All nodes in the database:")
+            result = await session.run("MATCH (n) RETURN labels(n) as labels, count(n) as count")
+            async for record in result:
+                print(f"   {record['labels']}: {record['count']}")
+            
+            # Check Memory nodes
+            print("\n2. Memory nodes:")
+            result = await session.run("MATCH (m:Memory) RETURN m.id as id, m.created_at as created_at")
+            async for record in result:
+                print(f"   Memory ID: {record['id']}")
+                print(f"   Created: {record['created_at']}")
+            
+            # Check Entity nodes
+            print("\n3. Entity nodes:")
+            result = await session.run("MATCH (e:Entity) RETURN e.name as name, e.type as type, e.properties_json as props")
+            async for record in result:
+                print(f"   Entity: {record['name']} ({record['type']})")
+                if record['props']:
+                    try:
+                        props = json.loads(record['props'])
+                        print(f"     Properties: {props}")
+                    except:
+                        print(f"     Properties: {record['props']}")
+            
+            # Check relationships
+            print("\n4. Relationships:")
+            result = await session.run("""
+                MATCH (m:Memory)-[r:RELATES_TO]->(e:Entity)
+                RETURN m.id as memory_id, r.relationship as relationship, 
+                       e.name as entity_name, r.confidence as confidence
+            """)
+            async for record in result:
+                print(f"   {record['memory_id'][:8]}... {record['relationship']} {record['entity_name']} (confidence: {record['confidence']})")
+            
+            # Full graph visualization query
+            print("\n5. Full graph structure:")
+            result = await session.run("""
+                MATCH (m:Memory)-[r:RELATES_TO]->(e:Entity)
+                RETURN m.id as memory_id, 
+                       r.relationship as relationship,
+                       e.name as entity_name,
+                       e.type as entity_type,
+                       r.confidence as confidence
+                ORDER BY r.confidence DESC
+            """)
+            
+            print("   Graph relationships (Memory → Entity):")
+            async for record in result:
+                print(f"     {record['memory_id'][:8]}... →[{record['relationship']}]→ {record['entity_name']} ({record['entity_type']}) [{record['confidence']}]")
+                
+        await driver.close()
+        
+        print("\n" + "=" * 50)
+        print("✅ Neo4j data check complete!")
+        print("🌐 Neo4j Browser: http://localhost:7474")
+        print("   Username: neo4j")
+        print("   Password: langmem_neo4j_password")
+        print("\n💡 Try these Cypher queries in Neo4j Browser:")
+        print("   MATCH (n) RETURN n")
+        print("   MATCH (m:Memory)-[r:RELATES_TO]->(e:Entity) RETURN m, r, e")
+        
+    except Exception as e:
+        print(f"❌ Error: {e}")
+
+if __name__ == "__main__":
+    asyncio.run(check_neo4j_data())