CONTRIBUTING.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
docs/CASCADE_WORKFLOW.md
docs/SEMANTIC_INDEX.yaml
docs/architecture/AI_WORKFLOW_AUTOMATION.md
docs/architecture/CHECK_SEMANTICS_FORMALIZATION.md
docs/architecture/CLI_DESIGN_PHILOSOPHY.md
docs/architecture/EPISTEMIC_ARCHITECTURE_ASSESSMENT.md
docs/architecture/EPISTEMIC_STATE_COMPLETE_CAPTURE.md
docs/architecture/EPISTEMIC_VECTOR_INTERPRETER.md
docs/architecture/INVESTIGATION_CYCLE_TRACKING.md
docs/architecture/MCO_INTEGRATION.md
docs/architecture/MEMORY_COMPACT_SPEC.md
docs/architecture/QDRANT_EPISTEMIC_INTEGRATION.md
docs/architecture/README.md
docs/architecture/REASONING_LAYER_ARCHITECTURE.md
docs/architecture/SEMANTIC_WORKFLOW_INDEX.md
docs/architecture/STORAGE_ARCHITECTURE_COMPLETE.md
docs/architecture/TUI_WORKFLOW_DASHBOARD_DESIGN.md
docs/architecture/epistemic_vs_git_diff.svg
docs/architecture/storage_architecture_flow.svg
docs/system-prompts/CANONICAL_SYSTEM_PROMPT.md
docs/system-prompts/CLAUDE.md
docs/system-prompts/COPILOT_INSTRUCTIONS.md
docs/system-prompts/CUSTOMIZATION_GUIDE.md
docs/system-prompts/GEMINI.md
docs/system-prompts/INSTALLATION.md
docs/system-prompts/QUICK_REFERENCE_WEB.md
docs/system-prompts/QWEN.md
docs/system-prompts/README.md
docs/system-prompts/instructions.md
empirica/__init__.py
empirica-mcp/test_epistemic.py
empirica-mcp/empirica_mcp/epistemic_middleware.py
empirica-mcp/empirica_mcp/server.py
empirica-mcp/empirica_mcp/epistemic/__init__.py
empirica-mcp/empirica_mcp/epistemic/cli_prompt_templates.py
empirica-mcp/empirica_mcp/epistemic/mcp_response_templates.py
empirica-mcp/empirica_mcp/epistemic/modes.py
empirica-mcp/empirica_mcp/epistemic/personality.py
empirica-mcp/empirica_mcp/epistemic/router.py
empirica-mcp/empirica_mcp/epistemic/shared_vector_semantics.py
empirica-mcp/empirica_mcp/epistemic/state_machine.py
empirica.egg-info/PKG-INFO
empirica.egg-info/SOURCES.txt
empirica.egg-info/dependency_links.txt
empirica.egg-info/entry_points.txt
empirica.egg-info/requires.txt
empirica.egg-info/top_level.txt
empirica/api/__init__.py
empirica/api/app.py
empirica/api/routes/__init__.py
empirica/api/routes/comparison.py
empirica/api/routes/deltas.py
empirica/api/routes/heatmaps.py
empirica/api/routes/sessions.py
empirica/api/routes/verification.py
empirica/cli/__init__.py
empirica/cli/__main__.py
empirica/cli/asyncio_fix.py
empirica/cli/cli_core.py
empirica/cli/cli_utils.py
empirica/cli/mcp_client.py
empirica/cli/simple_session_server.py
empirica/cli/uvl_formatter.py
empirica/cli/command_handlers/__init__.py
empirica/cli/command_handlers/action_commands.py
empirica/cli/command_handlers/ask_handler.py
empirica/cli/command_handlers/cascade_commands.py
empirica/cli/command_handlers/chat_handler.py
empirica/cli/command_handlers/checkpoint_commands.py
empirica/cli/command_handlers/checkpoint_signing_commands.py
empirica/cli/command_handlers/config_commands.py
empirica/cli/command_handlers/dashboard.py
empirica/cli/command_handlers/doc_commands.py
empirica/cli/command_handlers/edit_verification_command.py
empirica/cli/command_handlers/epistemics_commands.py
empirica/cli/command_handlers/goal_claim_command.py
empirica/cli/command_handlers/goal_commands.py
empirica/cli/command_handlers/goal_complete_command.py
empirica/cli/command_handlers/goal_discovery_commands.py
empirica/cli/command_handlers/goals_ready_command.py
empirica/cli/command_handlers/handoff_commands.py
empirica/cli/command_handlers/identity_commands.py
empirica/cli/command_handlers/investigation_commands.py
empirica/cli/command_handlers/issue_capture_commands.py
empirica/cli/command_handlers/mcp_commands.py
empirica/cli/command_handlers/mistake_commands.py
empirica/cli/command_handlers/modality_commands.py
empirica/cli/command_handlers/monitor_commands.py
empirica/cli/command_handlers/onboard.py
empirica/cli/command_handlers/onboard_handler.py
empirica/cli/command_handlers/performance_commands.py
empirica/cli/command_handlers/project_commands.py
empirica/cli/command_handlers/project_config_enrichment.py
empirica/cli/command_handlers/project_embed.py
empirica/cli/command_handlers/project_init.py
empirica/cli/command_handlers/project_search.py
empirica/cli/command_handlers/session_commands.py
empirica/cli/command_handlers/session_create.py
empirica/cli/command_handlers/skill_commands.py
empirica/cli/command_handlers/utility_commands.py
empirica/cli/command_handlers/vision_commands.py
empirica/cli/command_handlers/workflow_commands.py
empirica/cli/command_handlers/workspace_init.py
empirica/cli/parsers/__init__.py
empirica/cli/parsers/action_parsers.py
empirica/cli/parsers/cascade_parsers.py
empirica/cli/parsers/checkpoint_parsers.py
empirica/cli/parsers/config_parsers.py
empirica/cli/parsers/edit_verification_parsers.py
empirica/cli/parsers/epistemics_parsers.py
empirica/cli/parsers/investigation_parsers.py
empirica/cli/parsers/issue_capture_parsers.py
empirica/cli/parsers/monitor_parsers.py
empirica/cli/parsers/performance_parsers.py
empirica/cli/parsers/session_parsers.py
empirica/cli/parsers/skill_parsers.py
empirica/cli/parsers/user_interface_parsers.py
empirica/cli/parsers/utility_parsers.py
empirica/cli/parsers/vision_parsers.py
empirica/cli/utils/config_validator.py
empirica/cli/utils/project_resolver.py
empirica/cli/utils/workflow_suggestions.py
empirica/components/edit_verification/__init__.py
empirica/components/edit_verification/confidence_assessor.py
empirica/components/edit_verification/mcp_integration.py
empirica/components/edit_verification/strategy_executor.py
empirica/config/__init__.py
empirica/config/ai_registry.json
empirica/config/credentials_loader.py
empirica/config/database_config.py
empirica/config/goal_scope_loader.py
empirica/config/investigation_profiles.yaml
empirica/config/mco_loader.py
empirica/config/mcp_security.yaml
empirica/config/memory_gap_policy_loader.py
empirica/config/modality_config.yaml
empirica/config/path_resolver.py
empirica/config/profile_loader.py
empirica/config/project_config_loader.py
empirica/config/semantic_index_loader.py
empirica/config/threshold_loader.py
empirica/config/mco/MCO_INDEX.yaml
empirica/config/mco/ask_before_investigate.yaml
empirica/config/mco/bootstrap_triggers.yaml
empirica/config/mco/cascade_styles.yaml
empirica/config/mco/confidence_weights.yaml
empirica/config/mco/epistemic_conduct.yaml
empirica/config/mco/feedback_loops.yaml
empirica/config/mco/goal_scopes.yaml
empirica/config/mco/model_profiles.yaml
empirica/config/mco/personas.yaml
empirica/config/mco/protocols.yaml
empirica/core/__init__.py
empirica/core/checkpoint_signer.py
empirica/core/context_load_balancer.py
empirica/core/epistemic_bus.py
empirica/core/epistemic_trajectory.py
empirica/core/findings_deprecation.py
empirica/core/issue_capture.py
empirica/core/memory_gap_detector.py
empirica/core/signaling.py
empirica/core/thresholds.py
empirica/core/canonical/__init__.py
empirica/core/canonical/canonical_goal_orchestrator.py
empirica/core/canonical/git_enhanced_reflex_logger.py
empirica/core/canonical/goal_orchestrator_bridge.py
empirica/core/canonical/reflex_frame.py
empirica/core/canonical/reflex_logger.py
empirica/core/canonical/empirica_git/__init__.py
empirica/core/canonical/empirica_git/checkpoint_manager.py
empirica/core/canonical/empirica_git/goal_store.py
empirica/core/canonical/empirica_git/sentinel_hooks.py
empirica/core/canonical/empirica_git/session_sync.py
empirica/core/completion/__init__.py
empirica/core/completion/git_query.py
empirica/core/completion/tracker.py
empirica/core/completion/types.py
empirica/core/docs/doc_planner.py
empirica/core/drift/__init__.py
empirica/core/drift/mirror_drift_monitor.py
empirica/core/git_ops/__init__.py
empirica/core/git_ops/signed_operations.py
empirica/core/goals/__init__.py
empirica/core/goals/decision_logic.py
empirica/core/goals/repository.py
empirica/core/goals/types.py
empirica/core/goals/validation.py
empirica/core/handoff/__init__.py
empirica/core/handoff/auto_generator.py
empirica/core/handoff/report_generator.py
empirica/core/handoff/storage.py
empirica/core/identity/__init__.py
empirica/core/identity/ai_identity.py
empirica/core/identity/signature.py
empirica/core/metacognitive_cascade/__init__.py
empirica/core/metacognitive_cascade/investigation_plugin.py
empirica/core/metacognitive_cascade/investigation_strategy.py
empirica/core/metacognitive_cascade/metacognitive_cascade.py
empirica/core/persona/__init__.py
empirica/core/persona/persona_manager.py
empirica/core/persona/persona_profile.py
empirica/core/persona/signing_persona.py
empirica/core/persona/validation.py
empirica/core/persona/harness/__init__.py
empirica/core/persona/harness/communication.py
empirica/core/persona/harness/persona_harness.py
empirica/core/persona/schemas/persona_schema.json
empirica/core/persona/sentinel/__init__.py
empirica/core/persona/sentinel/arbitration_strategies.py
empirica/core/persona/sentinel/composition_strategies.py
empirica/core/persona/sentinel/orchestration_result.py
empirica/core/persona/sentinel/sentinel_orchestrator.py
empirica/core/persona/templates/__init__.py
empirica/core/qdrant/__init__.py
empirica/core/qdrant/embeddings.py
empirica/core/qdrant/persona_registry.py
empirica/core/qdrant/vector_store.py
empirica/core/schemas/__init__.py
empirica/core/schemas/assessment_converters.py
empirica/core/schemas/epistemic_assessment.py
empirica/core/skills/parser.py
empirica/core/tasks/__init__.py
empirica/core/tasks/repository.py
empirica/core/tasks/types.py
empirica/core/validation/__init__.py
empirica/core/validation/coherence_validator.py
empirica/core/validation/handoff_validator.py
empirica/core/validation/rehydration.py
empirica/core/validation/validation_utils.py
empirica/dashboard/__init__.py
empirica/dashboard/cascade_monitor.py
empirica/dashboard/snapshot_monitor.py
empirica/data/__init__.py
empirica/data/connection_pool.py
empirica/data/db_adapter.py
empirica/data/flow_state_calculator.py
empirica/data/session_database.py
empirica/data/session_json_handler.py
empirica/data/formatters/__init__.py
empirica/data/formatters/context_formatter.py
empirica/data/formatters/reflex_exporter.py
empirica/data/migrations/__init__.py
empirica/data/migrations/migration_runner.py
empirica/data/migrations/migrations.py
empirica/data/repositories/__init__.py
empirica/data/repositories/base.py
empirica/data/repositories/branches.py
empirica/data/repositories/breadcrumbs.py
empirica/data/repositories/cascades.py
empirica/data/repositories/goals.py
empirica/data/repositories/projects.py
empirica/data/repositories/sessions.py
empirica/data/repositories/utilities.py
empirica/data/repositories/vectors.py
empirica/data/schema/__init__.py
empirica/data/schema/epistemic_schema.py
empirica/data/schema/goals_schema.py
empirica/data/schema/projects_schema.py
empirica/data/schema/sessions_schema.py
empirica/data/schema/tracking_schema.py
empirica/integration/__init__.py
empirica/integration/empirica_action_hooks.py
empirica/integrations/branch_mapping.py
empirica/integrations/beads/__init__.py
empirica/integrations/beads/adapter.py
empirica/integrations/beads/config.py
empirica/investigation/__init__.py
empirica/investigation/investigation_plugin.py
empirica/investigation/advanced_investigation/__init__.py
empirica/investigation/advanced_investigation/advanced_investigation.py
empirica/metrics/__init__.py
empirica/metrics/flow_state.py
empirica/metrics/token_efficiency.py
empirica/plugins/__init__.py
empirica/plugins/base_plugin.py
empirica/plugins/dashboard_spawner.py
empirica/plugins/modality_switcher/__init__.py
empirica/plugins/modality_switcher/auth_manager.py
empirica/plugins/modality_switcher/config_loader.py
empirica/plugins/modality_switcher/domain_vectors.py
empirica/plugins/modality_switcher/epistemic_extractor.py
empirica/plugins/modality_switcher/epistemic_router.py
empirica/plugins/modality_switcher/epistemic_snapshot.py
empirica/plugins/modality_switcher/genuine_self_assessment.py
empirica/plugins/modality_switcher/modality_switcher.py
empirica/plugins/modality_switcher/plugin_manifest.json
empirica/plugins/modality_switcher/plugin_registry.py
empirica/plugins/modality_switcher/register_adapters.py
empirica/plugins/modality_switcher/snapshot_provider.py
empirica/plugins/modality_switcher/thinking_analyzer.py
empirica/plugins/modality_switcher/usage_monitor.py
empirica/plugins/modality_switcher/adapters/__init__.py
empirica/plugins/modality_switcher/adapters/copilot_adapter.py
empirica/plugins/modality_switcher/adapters/gemini_adapter.py
empirica/plugins/modality_switcher/adapters/minimax_adapter.py
empirica/plugins/modality_switcher/adapters/openrouter_adapter.py
empirica/plugins/modality_switcher/adapters/qodo_adapter.py
empirica/plugins/modality_switcher/adapters/qwen_adapter.py
empirica/plugins/modality_switcher/adapters/rovodev_adapter.py
empirica/plugins/modality_switcher/domain_vectors_custom/example_chemistry.py
empirica/reasoning/__init__.py
empirica/reasoning/epistemic_cascade.py
empirica/reasoning/ollama_adapter.py
empirica/reasoning/service.py
empirica/reasoning/types.py
empirica/schemas/check_config.json
empirica/schemas/preflight_config.json
empirica/tests/epistemic_checking/corpus/grounding_paper_check_result.json
empirica/tools/epistemic_checker.py
empirica/tools/epistemic_checker_v2.py
empirica/tui/__init__.py
empirica/tui/dashboard.py
empirica/utils/__init__.py
empirica/utils/cli_doc_validator.py
empirica/utils/deprecation_detector.py
empirica/utils/doc_code_integrity.py
empirica/utils/finding_refs.py
empirica/utils/session_resolver.py
empirica/utils/structure_health.py
empirica/vision/__init__.py
empirica/vision/readable_translator.py
empirica/vision/slide_processor.py