refactor: Major reorganization of optimization_engine module structure

BREAKING CHANGE: Module paths have been reorganized for better maintainability.
Backwards compatibility aliases with deprecation warnings are provided.

New Structure:
- core/           - Optimization runners (runner, intelligent_optimizer, etc.)
- processors/     - Data processing
  - surrogates/   - Neural network surrogates
- nx/             - NX/Nastran integration (solver, updater, session_manager)
- study/          - Study management (creator, wizard, state, reset)
- reporting/      - Reports and analysis (visualizer, report_generator)
- config/         - Configuration management (manager, builder)
- utils/          - Utilities (logger, auto_doc, etc.)
- future/         - Research/experimental code

Migration:
- ~200 import changes across 125 files
- All __init__.py files use lazy loading to avoid circular imports
- Backwards compatibility layer supports old import paths with warnings
- All existing functionality preserved

To migrate existing code:
  OLD: from optimization_engine.nx_solver import NXSolver
  NEW: from optimization_engine.nx.solver import NXSolver

  OLD: from optimization_engine.runner import OptimizationRunner
  NEW: from optimization_engine.core.runner import OptimizationRunner

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

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

tests/demo_research_agent.py

@@ -20,7 +20,7 @@ if sys.platform == 'win32':
 project_root = Path(__file__).parent.parent
 sys.path.insert(0, str(project_root))
 
-from optimization_engine.research_agent import (
+from optimization_engine.future.research_agent import (
     ResearchAgent,
     ResearchFindings,
     KnowledgeGap,

tests/interactive_optimization_setup.py

@@ -15,10 +15,10 @@ from pathlib import Path
 
 sys.path.insert(0, str(Path(__file__).parent.parent))
 
-from optimization_engine.optimization_setup_wizard import OptimizationSetupWizard
-from optimization_engine.llm_optimization_runner import LLMOptimizationRunner
-from optimization_engine.nx_solver import NXSolver
-from optimization_engine.nx_updater import NXParameterUpdater
+from optimization_engine.config.setup_wizard import OptimizationSetupWizard
+from optimization_engine.future.llm_optimization_runner import LLMOptimizationRunner
+from optimization_engine.nx.solver import NXSolver
+from optimization_engine.nx.updater import NXParameterUpdater
 
 
 def print_section(title: str):

tests/run_5trial_test.py

@@ -15,8 +15,8 @@ sys.path.insert(0, str(Path(__file__).parent.parent))
 import atomizer_paths
 atomizer_paths.ensure_imports()
 
-from optimization_engine.runner import OptimizationRunner
-from optimization_engine.nx_solver import run_nx_simulation
+from optimization_engine.core.runner import OptimizationRunner
+from optimization_engine.nx.solver import run_nx_simulation
 from optimization_engine.result_extractors.extractors import (
     stress_extractor,
     displacement_extractor

tests/run_beam_benchmarking.py

@@ -18,7 +18,7 @@ from pathlib import Path
 # Add parent directory to path
 sys.path.insert(0, str(Path(__file__).parent.parent))
 
-from optimization_engine.study_creator import StudyCreator
+from optimization_engine.study.creator import StudyCreator
 import logging
 
 # Setup logging

tests/run_beam_benchmarking_clean.py

@@ -18,7 +18,7 @@ from pathlib import Path
 # Add parent directory to path
 sys.path.insert(0, str(Path(__file__).parent.parent))
 
-from optimization_engine.study_creator import StudyCreator
+from optimization_engine.study.creator import StudyCreator
 import logging
 
 # Setup logging

tests/run_benchmarking_simple.py

@@ -8,7 +8,7 @@ from pathlib import Path
 
 sys.path.insert(0, str(Path(__file__).parent.parent))
 
-from optimization_engine.study_creator import StudyCreator
+from optimization_engine.study.creator import StudyCreator
 import logging
 
 logging.basicConfig(level=logging.INFO, format='%(levelname)s - %(message)s')

tests/setup_beam_optimization.py

@@ -13,7 +13,7 @@ from pathlib import Path
 
 sys.path.insert(0, str(Path(__file__).parent.parent))
 
-from optimization_engine.study_creator import StudyCreator
+from optimization_engine.study.creator import StudyCreator
 
 
 def main():

tests/test_api_verification.py

@@ -18,7 +18,7 @@ from pathlib import Path
 # Add parent directory to path
 sys.path.insert(0, str(Path(__file__).parent.parent))
 
-from optimization_engine.llm_workflow_analyzer import LLMWorkflowAnalyzer
+from optimization_engine.future.llm_workflow_analyzer import LLMWorkflowAnalyzer
 
 
 def test_api_connection():

tests/test_beam_workflow.py

@@ -20,7 +20,7 @@ from pathlib import Path
 # Add parent directory to path
 sys.path.insert(0, str(Path(__file__).parent.parent))
 
-from optimization_engine.study_creator import StudyCreator
+from optimization_engine.study.creator import StudyCreator
 import logging
 
 # Setup logging

tests/test_bracket_full_optimization.py

@@ -25,9 +25,9 @@ import json
 
 sys.path.insert(0, str(Path(__file__).parent.parent))
 
-from optimization_engine.llm_optimization_runner import LLMOptimizationRunner
-from optimization_engine.nx_solver import NXSolver
-from optimization_engine.nx_updater import NXParameterUpdater
+from optimization_engine.future.llm_optimization_runner import LLMOptimizationRunner
+from optimization_engine.nx.solver import NXSolver
+from optimization_engine.nx.updater import NXParameterUpdater
 
 # LLM workflow for bracket optimization
 llm_workflow = {

tests/test_bracket_llm_runner.py

@@ -17,7 +17,7 @@ from pathlib import Path
 
 sys.path.insert(0, str(Path(__file__).parent.parent))
 
-from optimization_engine.llm_optimization_runner import LLMOptimizationRunner
+from optimization_engine.future.llm_optimization_runner import LLMOptimizationRunner
 
 # LLM workflow for bracket optimization
 # Goal: Maximize displacement while keeping stress below safety factor

tests/test_cbar_genetic_algorithm.py

@@ -22,10 +22,10 @@ if sys.platform == 'win32':
 project_root = Path(__file__).parent.parent
 sys.path.insert(0, str(project_root))
 
-from optimization_engine.workflow_decomposer import WorkflowDecomposer
-from optimization_engine.step_classifier import StepClassifier
-from optimization_engine.codebase_analyzer import CodebaseCapabilityAnalyzer
-from optimization_engine.capability_matcher import CapabilityMatcher
+from optimization_engine.future.workflow_decomposer import WorkflowDecomposer
+from optimization_engine.future.step_classifier import StepClassifier
+from optimization_engine.utils.codebase_analyzer import CodebaseCapabilityAnalyzer
+from optimization_engine.config.capability_matcher import CapabilityMatcher
 
 
 def main():

tests/test_cbush_optimization.py

@@ -10,10 +10,10 @@ from pathlib import Path
 project_root = Path(__file__).parent.parent
 sys.path.insert(0, str(project_root))
 
-from optimization_engine.codebase_analyzer import CodebaseCapabilityAnalyzer
-from optimization_engine.workflow_decomposer import WorkflowDecomposer
-from optimization_engine.capability_matcher import CapabilityMatcher
-from optimization_engine.targeted_research_planner import TargetedResearchPlanner
+from optimization_engine.utils.codebase_analyzer import CodebaseCapabilityAnalyzer
+from optimization_engine.future.workflow_decomposer import WorkflowDecomposer
+from optimization_engine.config.capability_matcher import CapabilityMatcher
+from optimization_engine.future.targeted_research_planner import TargetedResearchPlanner
 
 
 def main():

tests/test_code_generation.py

@@ -26,7 +26,7 @@ if sys.platform == 'win32':
 project_root = Path(__file__).parent.parent
 sys.path.insert(0, str(project_root))
 
-from optimization_engine.research_agent import (
+from optimization_engine.future.research_agent import (
     ResearchAgent,
     ResearchFindings,
     CONFIDENCE_LEVELS

tests/test_complete_research_workflow.py

@@ -28,7 +28,7 @@ if sys.platform == 'win32':
 project_root = Path(__file__).parent.parent
 sys.path.insert(0, str(project_root))
 
-from optimization_engine.research_agent import (
+from optimization_engine.future.research_agent import (
     ResearchAgent,
     CONFIDENCE_LEVELS
 )

tests/test_complex_multiobj_request.py

@@ -11,10 +11,10 @@ from pathlib import Path
 project_root = Path(__file__).parent.parent
 sys.path.insert(0, str(project_root))
 
-from optimization_engine.codebase_analyzer import CodebaseCapabilityAnalyzer
-from optimization_engine.workflow_decomposer import WorkflowDecomposer
-from optimization_engine.capability_matcher import CapabilityMatcher
-from optimization_engine.targeted_research_planner import TargetedResearchPlanner
+from optimization_engine.utils.codebase_analyzer import CodebaseCapabilityAnalyzer
+from optimization_engine.future.workflow_decomposer import WorkflowDecomposer
+from optimization_engine.config.capability_matcher import CapabilityMatcher
+from optimization_engine.future.targeted_research_planner import TargetedResearchPlanner
 
 
 def main():

tests/test_hooks_with_bracket.py

@@ -17,7 +17,7 @@ sys.path.insert(0, str(Path(__file__).parent.parent))
 import atomizer_paths
 atomizer_paths.ensure_imports()
 
-from optimization_engine.runner import OptimizationRunner
+from optimization_engine.core.runner import OptimizationRunner
 from optimization_engine.result_extractors.extractors import (
     stress_extractor,
     displacement_extractor

tests/test_interactive_session.py

@@ -26,7 +26,7 @@ examples_path = project_root / "examples"
 sys.path.insert(0, str(examples_path))
 
 from interactive_research_session import InteractiveResearchSession
-from optimization_engine.research_agent import CONFIDENCE_LEVELS
+from optimization_engine.future.research_agent import CONFIDENCE_LEVELS
 
 
 def test_interactive_demo():

tests/test_journal_optimization.py

@@ -22,9 +22,9 @@ sys.path.insert(0, str(Path(__file__).parent.parent))
 import atomizer_paths
 atomizer_paths.ensure_imports()
 
-from optimization_engine.runner import OptimizationRunner
-from optimization_engine.nx_updater import update_nx_model
-from optimization_engine.nx_solver import run_nx_simulation
+from optimization_engine.core.runner import OptimizationRunner
+from optimization_engine.nx.updater import update_nx_model
+from optimization_engine.nx.solver import run_nx_simulation
 from optimization_engine.result_extractors.extractors import (
     stress_extractor,
     displacement_extractor

tests/test_knowledge_base_search.py

@@ -25,7 +25,7 @@ if sys.platform == 'win32':
 project_root = Path(__file__).parent.parent
 sys.path.insert(0, str(project_root))
 
-from optimization_engine.research_agent import (
+from optimization_engine.future.research_agent import (
     ResearchAgent,
     ResearchFindings,
     KnowledgeGap,

tests/test_llm_complex_request.py

@@ -29,7 +29,7 @@ if sys.platform == 'win32':
 project_root = Path(__file__).parent.parent
 sys.path.insert(0, str(project_root))
 
-from optimization_engine.llm_workflow_analyzer import LLMWorkflowAnalyzer
+from optimization_engine.future.llm_workflow_analyzer import LLMWorkflowAnalyzer
 
 
 def main():

tests/test_llm_runner_init.py

@@ -4,7 +4,7 @@ from pathlib import Path
 
 sys.path.insert(0, str(Path(__file__).parent.parent))
 
-from optimization_engine.llm_optimization_runner import LLMOptimizationRunner
+from optimization_engine.future.llm_optimization_runner import LLMOptimizationRunner
 
 # Example LLM workflow
 llm_workflow = {

tests/test_modal_deformation_request.py

@@ -28,7 +28,7 @@ if sys.platform == 'win32':
 project_root = Path(__file__).parent.parent
 sys.path.insert(0, str(project_root))
 
-from optimization_engine.research_agent import ResearchAgent
+from optimization_engine.future.research_agent import ResearchAgent
 
 
 def test_complex_modal_request():

tests/test_optimization_setup_wizard.py

@@ -16,7 +16,7 @@ from pathlib import Path
 
 sys.path.insert(0, str(Path(__file__).parent.parent))
 
-from optimization_engine.optimization_setup_wizard import OptimizationSetupWizard
+from optimization_engine.config.setup_wizard import OptimizationSetupWizard
 
 
 if __name__ == '__main__':

tests/test_phase_2_5_intelligent_gap_detection.py

@@ -24,10 +24,10 @@ if sys.platform == 'win32':
 project_root = Path(__file__).parent.parent
 sys.path.insert(0, str(project_root))
 
-from optimization_engine.codebase_analyzer import CodebaseCapabilityAnalyzer
-from optimization_engine.workflow_decomposer import WorkflowDecomposer
-from optimization_engine.capability_matcher import CapabilityMatcher
-from optimization_engine.targeted_research_planner import TargetedResearchPlanner
+from optimization_engine.utils.codebase_analyzer import CodebaseCapabilityAnalyzer
+from optimization_engine.future.workflow_decomposer import WorkflowDecomposer
+from optimization_engine.config.capability_matcher import CapabilityMatcher
+from optimization_engine.future.targeted_research_planner import TargetedResearchPlanner
 
 
 def print_header(text: str, char: str = "="):

tests/test_phase_3_2_llm_mode.py

@@ -19,7 +19,7 @@ from pathlib import Path
 # Add parent directory to path
 sys.path.insert(0, str(Path(__file__).parent.parent))
 
-from optimization_engine.llm_workflow_analyzer import LLMWorkflowAnalyzer
+from optimization_engine.future.llm_workflow_analyzer import LLMWorkflowAnalyzer
 
 
 def test_llm_workflow_analysis():

tests/test_research_agent.py

@@ -33,7 +33,7 @@ if sys.platform == 'win32':
 project_root = Path(__file__).parent.parent
 sys.path.insert(0, str(project_root))
 
-from optimization_engine.research_agent import (
+from optimization_engine.future.research_agent import (
     ResearchAgent,
     ResearchFindings,
     CONFIDENCE_LEVELS
@@ -194,7 +194,7 @@ def test_research_session_documentation():
     agent = ResearchAgent()
 
     # Simulate a complete research session
-    from optimization_engine.research_agent import KnowledgeGap, SynthesizedKnowledge
+    from optimization_engine.future.research_agent import KnowledgeGap, SynthesizedKnowledge
 
     gap = KnowledgeGap(
         missing_features=['material_xml_generator'],

tests/test_step_classifier.py

@@ -21,8 +21,8 @@ if sys.platform == 'win32':
 project_root = Path(__file__).parent.parent
 sys.path.insert(0, str(project_root))
 
-from optimization_engine.workflow_decomposer import WorkflowDecomposer
-from optimization_engine.step_classifier import StepClassifier
+from optimization_engine.future.workflow_decomposer import WorkflowDecomposer
+from optimization_engine.future.step_classifier import StepClassifier
 
 
 def main():

tests/test_task_1_2_integration.py

@@ -27,7 +27,7 @@ from typing import Dict, Any
 # Add parent directory to path
 sys.path.insert(0, str(Path(__file__).parent.parent))
 
-from optimization_engine.llm_optimization_runner import LLMOptimizationRunner
+from optimization_engine.future.llm_optimization_runner import LLMOptimizationRunner
 
 
 def create_mock_llm_workflow() -> Dict[str, Any]:

tests/test_timestamp_verification.py

@@ -10,7 +10,7 @@ import time
 
 sys.path.insert(0, str(Path(__file__).parent.parent))
 
-from optimization_engine.nx_solver import NXSolver
+from optimization_engine.nx.solver import NXSolver
 
 print("=" * 60)
 print("Testing timestamp verification fix")

tests/test_training_data_exporter.py

@@ -9,7 +9,7 @@ import json
 import tempfile
 import shutil
 from pathlib import Path
-from optimization_engine.training_data_exporter import TrainingDataExporter, create_exporter_from_config
+from optimization_engine.processors.surrogates.training_data_exporter import TrainingDataExporter, create_exporter_from_config
 
 
 class TestTrainingDataExporter: