LICENSE
MANIFEST.in
README.md
pyproject.toml
requirements.txt
setup.py
cortex_mcp/ACCOUNTABILITY_AUDIT.md
cortex_mcp/API_REFERENCE.md
cortex_mcp/AUTOMATION_DESIGN.md
cortex_mcp/AUTOMATION_IMPOSSIBLE_TOOLS.md
cortex_mcp/AUTOMATION_IMPOSSIBLE_TOOLS_SIMPLIFIED.md
cortex_mcp/BENCHMARK_IMPLEMENTATION_FIXES.md
cortex_mcp/BETA_RECRUITMENT.md
cortex_mcp/BETA_TEST_GUIDE.md
cortex_mcp/CLAUDE.md
cortex_mcp/CLAUDE_DESKTOP_SETUP.md
cortex_mcp/COMPREHENSIVE_VERIFICATION_REPORT.md
cortex_mcp/CORTEX_AUTOMATION_TEST_REPORT.md
cortex_mcp/FEATURE_VERIFICATION_REPORT.md
cortex_mcp/FEEDBACK_COLLECTION_SYSTEM.md
cortex_mcp/FINAL_PHASE_REPORT.md
cortex_mcp/GOAL_FEATURE_MAPPING.md
cortex_mcp/INSTALLATION.md
cortex_mcp/LOG_SYSTEM_REVIEW.md
cortex_mcp/MANUAL_TEST_GUIDE.md
cortex_mcp/MEMORY_BLOAT_FIX_REPORT.md
cortex_mcp/PERFORMANCE_TRADEOFF_ANALYSIS.md
cortex_mcp/PHASE9_COMPLETE_AUDIT.md
cortex_mcp/PHASE9_DIAGNOSIS.md
cortex_mcp/QA_TEST_PLAN.md
cortex_mcp/README.md
cortex_mcp/SKIP_TESTS.md
cortex_mcp/SYSTEM_PROMPT_MIGRATION_GUIDE.md
cortex_mcp/TELEMETRY_EVENTS_MAPPING.md
cortex_mcp/TELEMETRY_MASTER_PLAN.md
cortex_mcp/TELEMETRY_MIGRATION_v2.md
cortex_mcp/TELEMETRY_V2_FINAL_REPORT.md
cortex_mcp/ULTRATHINK_BLIND_SPOT_ANALYSIS.md
cortex_mcp/ULTRATHINK_VERIFICATION.md
cortex_mcp/VERSION_PINNING.md
cortex_mcp/__init__.py
cortex_mcp/__main__.py
cortex_mcp/answer.md
cortex_mcp/bench_test.md
cortex_mcp/cleanup_merged_files.py
cortex_mcp/cli.py
cortex_mcp/config.py
cortex_mcp/cortex_prompt.md
cortex_mcp/cortex_protocols.md
cortex_mcp/debug_rag_metadata.py
cortex_mcp/debug_roc_auc.py
cortex_mcp/debug_snapshot_restore.py
cortex_mcp/final_report.md
cortex_mcp/final_test.md
cortex_mcp/fix_memory_bloat.py
cortex_mcp/hal.md
cortex_mcp/main 2.py
cortex_mcp/main 3.py
cortex_mcp/main.py
cortex_mcp/performance_optimization.md
cortex_mcp/pytest_collect_output.txt
cortex_mcp/requirements.txt
cortex_mcp/run_final_tests.py
cortex_mcp/run_final_tests_v2.py
cortex_mcp/run_first_20_tests.py
cortex_mcp/setup_test_user.py
cortex_mcp/test_analysis.md
cortex_mcp/test_api_integration.py
cortex_mcp/test_cortex_setup.py
cortex_mcp/test_evidence_fix.py
cortex_mcp/test_failure_analysis.md
cortex_mcp/test_final_consistency.py
cortex_mcp/test_first_20.py
cortex_mcp/test_grounding_score_consistency.py
cortex_mcp/test_high3_git_diff.py
cortex_mcp/test_high4_performance.py
cortex_mcp/test_length_warning.py
cortex_mcp/test_mcp_telemetry_v2.py
cortex_mcp/test_merge_fix.py
cortex_mcp/test_performance.py
cortex_mcp/test_performance_comprehensive.py
cortex_mcp/test_performance_improvements.py
cortex_mcp/test_phase9_init_errors.py
cortex_mcp/test_phase9_live.py
cortex_mcp/test_phase9_performance.py
cortex_mcp/test_real_performance.py
cortex_mcp/test_real_telemetry.py
cortex_mcp/test_regex_extraction.py
cortex_mcp/test_research_logger_integration.py
cortex_mcp/test_result_history_report.md
cortex_mcp/test_singleton_simple.py
cortex_mcp/test_telemetry_activation.py
cortex_mcp/test_telemetry_e2e.py
cortex_mcp/test_v2_core.py
cortex_mcp/verify_cache_removal.py
cortex_mcp/verify_data.py
cortex_mcp/verify_evidence_graph_real.py
cortex_mcp/verify_path_collection.py
cortex_mcp/verify_phase10.py
cortex_mcp/verify_phase10_v2.py
cortex_mcp/verify_phase9_fixes.py
cortex_mcp/adapters/__init__.py
cortex_mcp/adapters/mcp_clients.py
cortex_mcp/core/__init__.py
cortex_mcp/core/accountability_handler.py
cortex_mcp/core/ai_judge.py
cortex_mcp/core/alpha_logger.py
cortex_mcp/core/approval_system.py
cortex_mcp/core/ast_analyzer.py
cortex_mcp/core/ast_parser.py
cortex_mcp/core/atomic_write.py
cortex_mcp/core/auto_compressor.py
cortex_mcp/core/auto_saver.py
cortex_mcp/core/auto_trigger.py
cortex_mcp/core/auto_verifier.py
cortex_mcp/core/automation_manager.py
cortex_mcp/core/background_processor.py
cortex_mcp/core/backup_manager.py
cortex_mcp/core/bayesian_updater.py
cortex_mcp/core/boundary_protection.py
cortex_mcp/core/branch_decision_engine.py
cortex_mcp/core/branch_matcher.py
cortex_mcp/core/claim_extractor.py
cortex_mcp/core/claim_verifier.py
cortex_mcp/core/cloud_sync.py
cortex_mcp/core/code_structure_analyzer.py
cortex_mcp/core/content_matcher.py
cortex_mcp/core/context_graph.py
cortex_mcp/core/context_manager.py
cortex_mcp/core/contradiction_detector.py
cortex_mcp/core/contradiction_detector_v2.py
cortex_mcp/core/control_state.py
cortex_mcp/core/crypto_utils.py
cortex_mcp/core/decorators.py
cortex_mcp/core/dependency_verifier.py
cortex_mcp/core/embedding_cache.py
cortex_mcp/core/evidence_collector.py
cortex_mcp/core/evidence_graph.py
cortex_mcp/core/evidence_graph_v2.py
cortex_mcp/core/evidence_matcher.py
cortex_mcp/core/evidence_store.py
cortex_mcp/core/extension_sync.py
cortex_mcp/core/fractal_analyzer.py
cortex_mcp/core/fuzzy_claim_analyzer.py
cortex_mcp/core/fuzzy_prompt.py
cortex_mcp/core/git_sync.py
cortex_mcp/core/github_auth.py
cortex_mcp/core/grounding_scorer.py
cortex_mcp/core/hallucination_constants.py
cortex_mcp/core/hardcode_detector.py
cortex_mcp/core/hierarchical_rag.py
cortex_mcp/core/initial_scanner.py
cortex_mcp/core/intent_cache.py
cortex_mcp/core/key_claims_manager.py
cortex_mcp/core/license_manager.py
cortex_mcp/core/memory_manager.py
cortex_mcp/core/method_existence_checker.py
cortex_mcp/core/multi_session_sync.py
cortex_mcp/core/ontology_engine.py
cortex_mcp/core/pay_attention.py
cortex_mcp/core/phase92_git_evidence.py
cortex_mcp/core/phase94_initial_scan.py
cortex_mcp/core/project_config.py
cortex_mcp/core/project_graph.py
cortex_mcp/core/promise_tracker.py
cortex_mcp/core/rag_engine.py
cortex_mcp/core/reference_history.py
cortex_mcp/core/refresh_manager.py
cortex_mcp/core/relationship_graph.py
cortex_mcp/core/research_logger.py
cortex_mcp/core/response_formatter.py
cortex_mcp/core/scan_optimizer.py
cortex_mcp/core/security_utils.py
cortex_mcp/core/semantic_relationship.py
cortex_mcp/core/semantic_web.py
cortex_mcp/core/shared_embedder.py
cortex_mcp/core/similarity_judge.py
cortex_mcp/core/smart_cache.py
cortex_mcp/core/smart_retrieval.py
cortex_mcp/core/team_merge.py
cortex_mcp/core/telemetry.py
cortex_mcp/core/telemetry_base.py
cortex_mcp/core/telemetry_client.py
cortex_mcp/core/telemetry_decorator.py
cortex_mcp/core/telemetry_events.py
cortex_mcp/core/telemetry_integration.py
cortex_mcp/core/telemetry_mcp.py
cortex_mcp/core/telemetry_storage.py
cortex_mcp/core/telemetry_wrapper.py
cortex_mcp/core/test_output_parser.py
cortex_mcp/core/thermodynamic_scorer.py
cortex_mcp/core/verification_pipeline.py
cortex_mcp/core/wave_interference_detector.py
cortex_mcp/core/memory/__init__.py
cortex_mcp/core/memory/branch_manager.py
cortex_mcp/core/memory/context_loader.py
cortex_mcp/core/memory/file_io.py
cortex_mcp/core/memory/hallucination_props.py
cortex_mcp/core/memory/index_handler.py
cortex_mcp/core/memory/misc_branch_analyzer.py
cortex_mcp/core/memory/node_manager.py
cortex_mcp/core/memory/summary_generator.py
cortex_mcp/core/memory/summary_helper.py
cortex_mcp/core/verifiers/__init__.py
cortex_mcp/core/verifiers/base.py
cortex_mcp/core/verifiers/code_element_verifier.py
cortex_mcp/core/verifiers/code_pattern_verifier.py
cortex_mcp/core/verifiers/evidence_collector.py
cortex_mcp/core/verifiers/file_change_verifier.py
cortex_mcp/core/verifiers/test_output_verifier.py
cortex_mcp/dashboard/__init__.py
cortex_mcp/dashboard/server.py
cortex_mcp/dashboard/templates/index.html
cortex_mcp/hooks/__init__.py
cortex_mcp/hooks/check_completion.py
cortex_mcp/hooks/detect_topic_shift.py
cortex_mcp/hooks/git_branch_changed.py
cortex_mcp/hooks/git_snapshot.py
cortex_mcp/hooks/inject_context.py
cortex_mcp/hooks/log_operation.py
cortex_mcp/hooks/runner.py
cortex_mcp/hooks/session_cleanup.py
cortex_mcp/hooks/session_init.py
cortex_mcp/hooks/validate_boundary.py
cortex_mcp/scripts/__init__.py
cortex_mcp/scripts/benchmark.py
cortex_mcp/scripts/export_stats.py
cortex_mcp/scripts/generate_report.py
cortex_mcp/scripts/install.py
cortex_mcp/scripts/license_cli.py
cortex_mcp/scripts/log_viewer.py
cortex_mcp/scripts/rebuild_semantic_web.py
cortex_mcp/scripts/recover_unregistered_branches.py
cortex_mcp/scripts/setup_cortex.py
cortex_mcp/scripts/setup_guide.py
cortex_mcp/scripts/test_mcp_protocol.py
cortex_mcp/scripts/test_phase4_git.py
cortex_mcp/scripts/verify_installation.py
cortex_mcp/tools/__init__.py
cortex_mcp/tools/auto_logging_wrapper.py
cortex_mcp/tools/cortex_tools.py
cortex_mcp/tools/verification_tools.py