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/debug_neo4j_relationships.py

@@ -0,0 +1,88 @@
+#!/usr/bin/env python3
+"""
+Debug Neo4j relationships to see what's happening
+"""
+
+import asyncio
+from neo4j import AsyncGraphDatabase
+
+# Configuration
+NEO4J_URL = "bolt://localhost:7687"
+NEO4J_USER = "neo4j"
+NEO4J_PASSWORD = "langmem_neo4j_password"
+
+async def debug_neo4j_relationships():
+    """Debug Neo4j relationships"""
+    print("🔍 Debugging Neo4j Relationships")
+    print("=" * 50)
+    
+    try:
+        driver = AsyncGraphDatabase.driver(NEO4J_URL, auth=(NEO4J_USER, NEO4J_PASSWORD))
+        
+        async with driver.session() as session:
+            # Check all relationship types
+            print("1. All relationship types in database:")
+            result = await session.run("CALL db.relationshipTypes()")
+            async for record in result:
+                print(f"   - {record[0]}")
+            
+            # Check all relationships
+            print("\n2. All relationships:")
+            result = await session.run("MATCH ()-[r]->() RETURN type(r) as rel_type, count(r) as count")
+            relationship_count = 0
+            async for record in result:
+                print(f"   {record['rel_type']}: {record['count']}")
+                relationship_count += record['count']
+            
+            if relationship_count == 0:
+                print("   No relationships found!")
+            
+            # Check MENTIONS relationships specifically
+            print("\n3. MENTIONS relationships:")
+            result = await session.run("MATCH (m:Memory)-[r:MENTIONS]->(e:Entity) RETURN m.id, e.name, e.type")
+            async for record in result:
+                print(f"   Memory {record['m.id'][:8]}... MENTIONS {record['e.name']} ({record['e.type']})")
+            
+            # Check all relationships with details
+            print("\n4. All relationships with details:")
+            result = await session.run("""
+                MATCH (a)-[r]->(b) 
+                RETURN labels(a)[0] as source_label, 
+                       coalesce(a.name, a.id) as source_name,
+                       type(r) as relationship,
+                       labels(b)[0] as target_label,
+                       coalesce(b.name, b.id) as target_name,
+                       r.confidence as confidence
+                ORDER BY relationship
+            """)
+            
+            async for record in result:
+                print(f"   {record['source_label']} '{record['source_name'][:20]}...' ")
+                print(f"   →[{record['relationship']}]→ ")
+                print(f"   {record['target_label']} '{record['target_name'][:20]}...' (conf: {record['confidence']})")
+                print()
+            
+            # Check if there are any dynamic relationships
+            print("\n5. Looking for dynamic relationships (non-MENTIONS):")
+            result = await session.run("""
+                MATCH (a)-[r]->(b) 
+                WHERE type(r) <> 'MENTIONS'
+                RETURN type(r) as rel_type, count(r) as count
+            """)
+            
+            found_dynamic = False
+            async for record in result:
+                print(f"   {record['rel_type']}: {record['count']}")
+                found_dynamic = True
+            
+            if not found_dynamic:
+                print("   No dynamic relationships found!")
+                print("   This suggests the AI relationship creation might have issues.")
+                
+        await driver.close()
+        
+    except Exception as e:
+        print(f"❌ Error: {e}")
+
+if __name__ == "__main__":
+    asyncio.run(debug_neo4j_relationships())