refactor(api): use sessionmaker in workflow & RAG pipeline services

[carlos4s]

Summary

• Replace with Session(bind=db.engine) as session, session.begin(): + session.commit() with
  sessionmaker(bind=db.engine).begin() in workflow_service and rag_pipeline
• Replace with Session(bind=engine, expire_on_commit=False) + session.commit() with
  sessionmaker(bind=engine, expire_on_commit=False).begin() in workflow_draft_variable_service
• Read-only session blocks left unchanged
• No test changes needed

Part of #24245

Test plan

• ruff check passes
• 108 workflow_service tests pass
• 249 rag_pipeline tests pass

[github-actions]

Pyrefly Diff

No changes detected.