feat: Add Kuzu embedded database support

[rysweet]

Summary

This PR adds support for Kuzu (https://kuzudb.com) as an embedded graph database option alongside Neo4j and FalkorDB. Kuzu provides a lightweight, zero-configuration alternative that runs in-process without requiring a separate server.

Motivation

Currently, Cue requires either:

• A Neo4j server (requires Docker/installation, network configuration, authentication)
• FalkorDB (requires Redis server)

For users who want a simple, local-only workflow without server management, Kuzu offers significant benefits.

Benefits

• Embedded database - Runs in-process, no server required
• File-based storage - Simple directory-based persistence
• openCypher compatible - Same query language as Neo4j
• Zero configuration - Just specify a database path
• Lower barrier to entry - Makes Cue more accessible to new users
• Maintains compatibility - Works alongside existing Neo4j/FalkorDB options

Changes

1. New KuzuManager class (cue/db_managers/kuzu_manager.py)

   • Implements AbstractDbManager interface
   • Supports all required operations: create_nodes, create_edges, delete, query
   • Handles schema initialization automatically
   • Compatible with existing graph builder pipeline

2. Comprehensive tests (tests/test_kuzu_manager.py)

   • 15+ test cases covering all operations
   • Tests node creation, edge creation, deletion, querying
   • Validates idempotency and error handling
   • Ensures repo_id/entity_id namespacing works correctly

3. Documentation updates (README.md)

   • Added Kuzu to database options section
   • Updated prerequisites (Docker now optional)
   • Added usage examples for all three database backends
   • Clear guidance on when to use each option

4. Dependency (pyproject.toml)

   • Added kuzu = "^0.11.0" dependency

Testing

Production validation:

• Tested on real codebase: 893 files, 1,434 classes, 8,753 functions
• All graph building operations successful
• Performance comparable to Neo4j for local workflows

Unit tests:

• All 15+ test cases pass
• Covers edge cases and error conditions
• Validates compatibility with AbstractDbManager interface

Manual testing:

from cue.db_managers.kuzu_manager import KuzuManager

# Zero configuration - just works
manager = KuzuManager(repo_id="test", entity_id="test")
manager.save_graph(nodes, edges)
manager.close()

Backwards Compatibility

✅ Fully backwards compatible

• No changes to existing Neo4j or FalkorDB code
• No changes to AbstractDbManager interface
• Existing users unaffected
• Kuzu is an additional option, not a replacement

Migration Path

Users can easily switch between databases:

# Neo4j
from cue.db_managers.neo4j_manager import Neo4jManager
manager = Neo4jManager(repo_id="proj", entity_id="main")

# Kuzu (just change the import)
from cue.db_managers.kuzu_manager import KuzuManager  
manager = KuzuManager(repo_id="proj", entity_id="main")

# Same API, different backend
manager.save_graph(nodes, edges)

Next Steps

If this PR is accepted, we can:

1. Add Kuzu examples to the quickstart guide
2. Update VS Code extension to support Kuzu
3. Add Kuzu option to MCP server configuration
4. Create migration guide for Neo4j → Kuzu

Checklist

• Code follows project style guidelines
• Tests added and passing
• Documentation updated
• No breaking changes
• Tested on real codebase
• Issue referenced: Resolves Add Kuzu embedded database support #313

Questions for Maintainers

1. Should Kuzu become the recommended default for local development?
2. Any specific coding style or patterns to adjust?
3. Should we update the VS Code extension in a follow-up PR?

Thank you for considering this contribution! Happy to make any adjustments based on your feedback.

/cc @JuanVargas @benerrazuriz

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