LICENSE
MANIFEST.in
README.md
pyproject.toml
docs/ALZHEIMER_DEMENTIA_DYNAMICS.md
docs/ALZHEIMER_DEMENTIA_IMPLEMENTATION.md
docs/API_REFERENCE.md
docs/ARCHITECTURE.md
docs/ARCHITECTURE_STRUCTURE.md
docs/COGNITIVE_BIAS_FIELD.md
docs/COGNITIVE_DYSFUNCTION.md
docs/COGNITIVE_LOOPS_ANALYSIS.md
docs/COGNITIVE_STATES.md
docs/COGNITIVE_STATES_HONEST.md
docs/COMPLETION_STATUS.md
docs/CURRENT_STATUS_AND_RECOMMENDATION.md
docs/DEMENTIA_ALZHEIMER_IMPLEMENTATION.md
docs/DEMO_LIMITATIONS.md
docs/DISORDER_SPECTRUM_ANALYSIS.md
docs/DYNAMICS_ENGINE_COMPLETE.md
docs/DYNAMICS_ENGINE_DEPLOYMENT_ANALYSIS.md
docs/DYNAMICS_ENGINE_FINAL_STATUS.md
docs/DYNAMICS_ENGINE_FUNCTIONS.md
docs/DYNAMICS_ENGINE_INTEGRATION_STATUS.md
docs/DYNAMICS_ENGINE_LOCATION.md
docs/DYNAMICS_ENGINE_STATUS.md
docs/ENGINE_STRUCTURE_ANALYSIS.md
docs/FOLDER_STRUCTURE_RECOMMENDATION.md
docs/IMPLEMENTATION_STATUS_COLD.md
docs/INTEGRATION_STATUS.md
docs/LONG_TERM_MEMORY.md
docs/MAXWELL_STRUCTURE.md
docs/MINIMAL_DYNAMICS_MODEL.md
docs/MODULARITY_ANALYSIS.md
docs/MODULARITY_IMPROVEMENTS.md
docs/PHYSICAL_DYNAMICS.md
docs/QUICK_DECISION_GUIDE.md
docs/README.md
docs/RELEASE_CHECKLIST.md
docs/ROADMAP.md
docs/STABILITY_CORE.md
docs/STRATEGIC_ANALYSIS.md
docs/TEST_RESULTS.md
docs/VERIFICATION_STATUS.md
docs/VERSION_STRATEGY.md
docs/archive/DEPLOYMENT_READY.md
docs/archive/DYNAMICS_ENGINE_COMPLETE.md
docs/archive/NEXT_STEPS.md
docs/archive/README.md
docs/archive/TECHNICAL_TASKS.md
docs/archive/TODO_NEXT.md
docs/development/ARCHIVE_STRUCTURE.md
docs/development/DEVELOPMENT_LOG.md
docs/development/WORK_LOG_2026_01_31.md
docs/technical/CODE_DOCUMENTATION.md
docs/technical/MAXWELL_IMPLEMENTATION_STATUS.md
docs/technical/SYSTEM_PHILOSOPHY.md
docs/version_history/PHAM_BLOCKCHAIN_LOG.md
docs/version_history/PHAM_DYNAMICS_v2.0.2.md
docs/version_history/VERSION_HISTORY.md
docs/work/CURRENT_WORK_STATUS.md
docs/work/DISORDER_ANALYSIS.md
docs/work/WORK_ANALYSIS.md
docs/work/WORK_COMPLETED.md
src/cognitive_kernel/__init__.py
src/cognitive_kernel/cognitive_modes.py
src/cognitive_kernel/core.py
src/cognitive_kernel/pipeline.py
src/cognitive_kernel/vector_integration.py
src/cognitive_kernel.egg-info/PKG-INFO
src/cognitive_kernel.egg-info/SOURCES.txt
src/cognitive_kernel.egg-info/dependency_links.txt
src/cognitive_kernel.egg-info/requires.txt
src/cognitive_kernel.egg-info/top_level.txt
src/cognitive_kernel/engines/__init__.py
src/cognitive_kernel/engines/interfaces.py
src/cognitive_kernel/engines/amygdala/__init__.py
src/cognitive_kernel/engines/amygdala/amygdala_engine.py
src/cognitive_kernel/engines/amygdala/config.py
src/cognitive_kernel/engines/amygdala/data_types.py
src/cognitive_kernel/engines/amygdala/fear_learning.py
src/cognitive_kernel/engines/basal_ganglia/__init__.py
src/cognitive_kernel/engines/basal_ganglia/basal_ganglia_engine.py
src/cognitive_kernel/engines/basal_ganglia/config.py
src/cognitive_kernel/engines/basal_ganglia/data_types.py
src/cognitive_kernel/engines/dynamics/__init__.py
src/cognitive_kernel/engines/dynamics/config.py
src/cognitive_kernel/engines/dynamics/dynamics_engine.py
src/cognitive_kernel/engines/dynamics/models.py
src/cognitive_kernel/engines/hypothalamus/__init__.py
src/cognitive_kernel/engines/hypothalamus/config.py
src/cognitive_kernel/engines/hypothalamus/data_types.py
src/cognitive_kernel/engines/hypothalamus/hpa_dynamics.py
src/cognitive_kernel/engines/hypothalamus/hypothalamus_engine.py
src/cognitive_kernel/engines/memoryrank/__init__.py
src/cognitive_kernel/engines/memoryrank/config.py
src/cognitive_kernel/engines/memoryrank/memoryrank_engine.py
src/cognitive_kernel/engines/memoryrank/persistence.py
src/cognitive_kernel/engines/memoryrank/pham_chain_persistence.json
src/cognitive_kernel/engines/panorama/__init__.py
src/cognitive_kernel/engines/panorama/config.py
src/cognitive_kernel/engines/panorama/panorama_engine.py
src/cognitive_kernel/engines/panorama/persistence.py
src/cognitive_kernel/engines/panorama/pham_chain_persistence.json
src/cognitive_kernel/engines/pfc/__init__.py
src/cognitive_kernel/engines/pfc/config.py
src/cognitive_kernel/engines/pfc/models.py
src/cognitive_kernel/engines/pfc/pfc_engine.py
src/cognitive_kernel/engines/thalamus/__init__.py
src/cognitive_kernel/engines/thalamus/config.py
src/cognitive_kernel/engines/thalamus/data_types.py
src/cognitive_kernel/engines/thalamus/thalamus_engine.py
tests/test_mathematical_models.py