fix: prevent SQLite corruption in parallel mode with atomic operations

Replace ineffective threading.Lock() with atomic SQL operations for
cross-process safety. Key changes:

- Add SQLAlchemy event hooks (do_connect/do_begin) for BEGIN IMMEDIATE
  transactions in api/database.py
- Add atomic_transaction() context manager for multi-statement ops
- Convert all feature MCP write operations to atomic UPDATE...WHERE
  with compare-and-swap patterns (feature_claim, mark_passing, etc.)
- Add WHERE passes=0 state guard to feature_mark_passing
- Add WAL checkpoint on shutdown and idempotent cleanup() in
  parallel_orchestrator.py with async-safe signal handling
- Wrap SQLite connections with contextlib.closing() in progress.py
- Add thread-safe engine cache with double-checked locking in
  assistant_database.py
- Migrate to SQLAlchemy 2.0 DeclarativeBase across all modules

Inspired by PR #108 (cabana8471-arch), with fixes for nested
BEGIN EXCLUSIVE bug and missing state guards.

Closes #106

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

registry.py

@@ -17,8 +17,7 @@ from pathlib import Path
 from typing import Any
 
 from sqlalchemy import Column, DateTime, Integer, String, create_engine, text
-from sqlalchemy.ext.declarative import declarative_base
-from sqlalchemy.orm import sessionmaker
+from sqlalchemy.orm import DeclarativeBase, sessionmaker
 
 # Module logger
 logger = logging.getLogger(__name__)
@@ -75,7 +74,9 @@ class RegistryPermissionDenied(RegistryError):
 # SQLAlchemy Model
 # =============================================================================
 
-Base = declarative_base()
+class Base(DeclarativeBase):
+    """SQLAlchemy 2.0 style declarative base."""
+    pass
 
 
 class Project(Base):