├── .github ├── pull_request_template.md └── workflows │ └── docs.yml ├── .gitignore ├── CHANGELOG.md ├── LICENSE.txt ├── README.md ├── RELEASE_NOTES.md ├── TESTING_GUIDE.md ├── docs ├── LOCAL_TESTING.md ├── Makefile ├── config.yml ├── launch_docs.py ├── resources │ └── other │ │ ├── COMMENTS.md │ │ ├── COMMIT_ORGANIZATION.md │ │ ├── DOCSTRINGS.md │ │ ├── PRE_MERGE_CLEANUP.md │ │ ├── RELEASE_WORKFLOW.md │ │ ├── UPDATE_DOCS.md │ │ └── see_also.md └── source │ ├── _static │ ├── custom.css │ ├── js │ │ └── execution_plan_viewer.js │ ├── logo.svg │ ├── resources │ │ ├── als_assistant │ │ │ ├── ALS_assistant_logo.png │ │ │ ├── fig_ALS_PV_Finder_MCP.pdf │ │ │ ├── fig_ALS_PV_finder.pdf │ │ │ ├── fig_ALS_experiment.png │ │ │ ├── fig_ALS_langfuse.pdf │ │ │ ├── fig_ALS_python.pdf │ │ │ └── fig_ALS_setup.pdf │ │ ├── execution_plans │ │ │ └── accelerator_assistant_execution_plan.json │ │ └── workflow_overview.pdf │ └── screenshots │ │ ├── channel_finder_db_preview_hierachical.png │ │ ├── channel_finder_db_preview_in_context.png │ │ ├── channel_finder_hierachical_cli.png │ │ ├── channel_finder_in_context_cli.png │ │ └── openwebui_demo.png │ ├── api_reference │ ├── 01_core_framework │ │ ├── 01_base_components.rst │ │ ├── 02_state_and_context.rst │ │ ├── 03_registry_system.rst │ │ ├── 04_configuration_system.rst │ │ ├── 05_prompt_management.rst │ │ ├── 06_command_system.rst │ │ └── index.rst │ ├── 02_infrastructure │ │ ├── 01_gateway.rst │ │ ├── 02_task-extraction.rst │ │ ├── 03_classification.rst │ │ ├── 04_orchestration.rst │ │ ├── 05_execution-control.rst │ │ ├── 06_message-generation.rst │ │ └── index.rst │ ├── 03_production_systems │ │ ├── 01_human-approval.rst │ │ ├── 02_data-management.rst │ │ ├── 03_python-execution.rst │ │ ├── 04_memory-storage.rst │ │ ├── 05_container-management.rst │ │ ├── 06_control-system-connectors.rst │ │ ├── _autosummary │ │ │ ├── deployment.container_manager.rst │ │ │ ├── deployment.loader.rst │ │ │ ├── framework.approval.ApprovalDecision.rst │ │ │ ├── framework.approval.ApprovalManager.rst │ │ │ ├── framework.approval.ApprovalMode.rst │ │ │ ├── framework.approval.GlobalApprovalConfig.rst │ │ │ ├── framework.approval.MemoryApprovalConfig.rst │ │ │ ├── framework.approval.MemoryApprovalEvaluator.rst │ │ │ ├── framework.approval.PythonExecutionApprovalConfig.rst │ │ │ ├── framework.approval.PythonExecutionApprovalEvaluator.rst │ │ │ ├── framework.approval.create_approval_type.rst │ │ │ ├── framework.approval.create_code_approval_interrupt.rst │ │ │ ├── framework.approval.create_memory_approval_interrupt.rst │ │ │ ├── framework.approval.create_plan_approval_interrupt.rst │ │ │ ├── framework.approval.get_approval_manager.rst │ │ │ ├── framework.approval.get_approval_resume_data.rst │ │ │ ├── framework.data_management.DataRetrievalResult.rst │ │ │ ├── framework.data_management.DataSourceContext.rst │ │ │ ├── framework.data_management.DataSourceManager.rst │ │ │ ├── framework.data_management.DataSourceProvider.rst │ │ │ ├── framework.data_management.DataSourceRequest.rst │ │ │ ├── framework.data_management.DataSourceRequester.rst │ │ │ ├── framework.data_management.create_data_source_request.rst │ │ │ ├── framework.data_management.get_data_source_manager.rst │ │ │ ├── framework.services.memory_storage.MemoryContent.rst │ │ │ ├── framework.services.memory_storage.MemoryStorageManager.rst │ │ │ ├── framework.services.memory_storage.UserMemoryProvider.rst │ │ │ ├── framework.services.memory_storage.get_memory_storage_manager.rst │ │ │ ├── framework.services.python_executor.CodeGenerationError.rst │ │ │ ├── framework.services.python_executor.CodeRuntimeError.rst │ │ │ ├── framework.services.python_executor.ContainerConnectivityError.rst │ │ │ ├── framework.services.python_executor.ContainerEndpointConfig.rst │ │ │ ├── framework.services.python_executor.ErrorCategory.rst │ │ │ ├── framework.services.python_executor.ExecutionControlConfig.rst │ │ │ ├── framework.services.python_executor.ExecutionModeConfig.rst │ │ │ ├── framework.services.python_executor.ExecutionTimeoutError.rst │ │ │ ├── framework.services.python_executor.NotebookAttempt.rst │ │ │ ├── framework.services.python_executor.NotebookType.rst │ │ │ ├── framework.services.python_executor.PythonExecutionContext.rst │ │ │ ├── framework.services.python_executor.PythonExecutionRequest.rst │ │ │ ├── framework.services.python_executor.PythonExecutionState.rst │ │ │ ├── framework.services.python_executor.PythonExecutionSuccess.rst │ │ │ ├── framework.services.python_executor.PythonExecutorException.rst │ │ │ ├── framework.services.python_executor.PythonExecutorService.rst │ │ │ └── framework.services.python_executor.PythonServiceResult.rst │ │ └── index.rst │ ├── 04_error_handling │ │ ├── 01_classification_system.rst │ │ ├── 02_exception_reference.rst │ │ ├── 03_recovery_coordination.rst │ │ └── index.rst │ ├── 05_framework_utilities │ │ └── index.rst │ └── index.rst │ ├── conf.py │ ├── contributing │ └── index.rst │ ├── developer-guides │ ├── 01_understanding-the-framework │ │ ├── 01_infrastructure-architecture.rst │ │ ├── 02_convention-over-configuration.rst │ │ ├── 03_langgraph-integration.rst │ │ ├── 04_orchestrator-first-philosophy.rst │ │ └── index.rst │ ├── 02_quick-start-patterns │ │ ├── 00_cli-reference.rst │ │ ├── 01_building-your-first-capability.rst │ │ ├── 02_state-and-context-essentials.rst │ │ ├── 03_running-and-testing.rst │ │ ├── 04_mcp-capability-generation.rst │ │ └── index.rst │ ├── 03_core-framework-systems │ │ ├── 01_state-management-architecture.rst │ │ ├── 02_context-management-system.rst │ │ ├── 03_registry-and-discovery.rst │ │ ├── 04_prompt-customization.rst │ │ ├── 05_message-and-execution-flow.rst │ │ ├── 06_configuration-architecture.rst │ │ └── index.rst │ ├── 04_infrastructure-components │ │ ├── 01_gateway-architecture.rst │ │ ├── 02_task-extraction-system.rst │ │ ├── 03_classification-and-routing.rst │ │ ├── 04_orchestrator-planning.rst │ │ ├── 05_message-generation.rst │ │ ├── 06_error-handling-infrastructure.rst │ │ └── index.rst │ ├── 05_production-systems │ │ ├── 01_human-approval-workflows.rst │ │ ├── 02_data-source-integration.rst │ │ ├── 03_python-execution-service │ │ │ ├── generator-basic.rst │ │ │ ├── generator-claude.rst │ │ │ ├── generator-mock.rst │ │ │ ├── index.rst │ │ │ └── service-overview.rst │ │ ├── 04_memory-storage-service.rst │ │ ├── 05_container-and-deployment.rst │ │ ├── 06_control-system-integration.rst │ │ └── index.rst │ ├── index.rst │ └── migration-guide-instance-methods.rst │ ├── example-applications │ ├── als-assistant.rst │ └── index.rst │ ├── getting-started │ ├── conceptual-tutorial.rst │ ├── control-assistant-part1-setup.rst │ ├── control-assistant-part2-channel-finder.rst │ ├── control-assistant-part3-production.rst │ ├── control-assistant-part4-customization.rst │ ├── control-assistant.rst │ ├── hello-world-tutorial.rst │ ├── index.rst │ └── installation.rst │ └── index.rst ├── env.example ├── pyproject.toml ├── pytest.ini ├── src ├── osprey │ ├── __init__.py │ ├── approval │ │ ├── __init__.py │ │ ├── approval_manager.py │ │ ├── approval_system.py │ │ ├── config_models.py │ │ └── evaluators.py │ ├── base │ │ ├── __init__.py │ │ ├── capability.py │ │ ├── decorators.py │ │ ├── errors.py │ │ ├── examples.py │ │ ├── nodes.py │ │ ├── planning.py │ │ └── results.py │ ├── capabilities │ │ ├── memory.py │ │ ├── python.py │ │ └── time_range_parsing.py │ ├── cli │ │ ├── __init__.py │ │ ├── chat_cmd.py │ │ ├── config_cmd.py │ │ ├── deploy_cmd.py │ │ ├── export_config_cmd.py │ │ ├── generate_cmd.py │ │ ├── health_cmd.py │ │ ├── init_cmd.py │ │ ├── interactive_menu.py │ │ ├── main.py │ │ ├── preview_styles.py │ │ ├── project_utils.py │ │ ├── registry_cmd.py │ │ ├── remove_cmd.py │ │ ├── styles.py │ │ └── templates.py │ ├── commands │ │ ├── __init__.py │ │ ├── categories.py │ │ ├── completer.py │ │ ├── registry.py │ │ └── types.py │ ├── connectors │ │ ├── __init__.py │ │ ├── archiver │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── epics_archiver_connector.py │ │ │ └── mock_archiver_connector.py │ │ ├── control_system │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── epics_connector.py │ │ │ └── mock_connector.py │ │ └── factory.py │ ├── context │ │ ├── __init__.py │ │ ├── base.py │ │ ├── context_manager.py │ │ └── loader.py │ ├── data_management │ │ ├── __init__.py │ │ ├── manager.py │ │ ├── providers.py │ │ └── request.py │ ├── deployment │ │ ├── __init__.py │ │ ├── container_manager.py │ │ ├── loader.py │ │ └── runtime_helper.py │ ├── generators │ │ ├── __init__.py │ │ ├── base_generator.py │ │ ├── config_updater.py │ │ ├── generate_from_mcp.py │ │ ├── generate_from_prompt.py │ │ ├── mcp_server_template.py │ │ ├── models.py │ │ └── registry_updater.py │ ├── graph │ │ ├── __init__.py │ │ └── graph_builder.py │ ├── infrastructure │ │ ├── clarify_node.py │ │ ├── classification_node.py │ │ ├── error_node.py │ │ ├── gateway.py │ │ ├── orchestration_node.py │ │ ├── respond_node.py │ │ ├── router_node.py │ │ └── task_extraction_node.py │ ├── interfaces │ │ ├── __init__.py │ │ └── cli │ │ │ ├── __init__.py │ │ │ └── direct_conversation.py │ ├── models │ │ ├── __init__.py │ │ ├── completion.py │ │ ├── factory.py │ │ ├── logging.py │ │ └── providers │ │ │ ├── __init__.py │ │ │ ├── anthropic.py │ │ │ ├── argo.py │ │ │ ├── base.py │ │ │ ├── cborg.py │ │ │ ├── google.py │ │ │ ├── ollama.py │ │ │ ├── openai.py │ │ │ └── stanford.py │ ├── prompts │ │ ├── __init__.py │ │ ├── base.py │ │ ├── defaults │ │ │ ├── __init__.py │ │ │ ├── clarification.py │ │ │ ├── classification.py │ │ │ ├── error_analysis.py │ │ │ ├── memory_extraction.py │ │ │ ├── orchestrator.py │ │ │ ├── python.py │ │ │ ├── response_generation.py │ │ │ ├── task_extraction.py │ │ │ └── time_range_parsing.py │ │ └── loader.py │ ├── registry │ │ ├── __init__.py │ │ ├── base.py │ │ ├── helpers.py │ │ ├── manager.py │ │ └── registry.py │ ├── runtime │ │ └── __init__.py │ ├── services │ │ ├── __init__.py │ │ ├── memory_storage │ │ │ ├── __init__.py │ │ │ ├── memory_provider.py │ │ │ ├── models.py │ │ │ └── storage_manager.py │ │ └── python_executor │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── analysis │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── node.py │ │ │ ├── pattern_detection.py │ │ │ └── policy_analyzer.py │ │ │ ├── approval │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ └── node.py │ │ │ ├── config.py │ │ │ ├── exceptions.py │ │ │ ├── execution │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── container_engine.py │ │ │ ├── control.py │ │ │ ├── limits_validator.py │ │ │ ├── node.py │ │ │ └── wrapper.py │ │ │ ├── generation │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── basic_generator.py │ │ │ ├── claude_code_generator.py │ │ │ ├── factory.py │ │ │ ├── interface.py │ │ │ ├── mock_generator.py │ │ │ └── node.py │ │ │ ├── models.py │ │ │ ├── service.py │ │ │ └── services.py │ ├── state │ │ ├── __init__.py │ │ ├── control.py │ │ ├── execution.py │ │ ├── messages.py │ │ ├── session.py │ │ ├── state.py │ │ └── state_manager.py │ ├── templates │ │ ├── __init__.py │ │ ├── apps │ │ │ ├── __init__.py │ │ │ ├── control_assistant │ │ │ │ ├── README.md.j2 │ │ │ │ ├── __init__.py │ │ │ │ ├── _agent_data │ │ │ │ │ └── example_scripts │ │ │ │ │ │ └── plotting │ │ │ │ │ │ ├── README.md │ │ │ │ │ │ ├── aligned_multiple_plots.py │ │ │ │ │ │ ├── multi_subplot.py │ │ │ │ │ │ ├── publication_quality.py │ │ │ │ │ │ └── time_series_basic.py │ │ │ │ ├── capabilities │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── archiver_retrieval.py.j2 │ │ │ │ │ ├── channel_finding.py.j2 │ │ │ │ │ ├── channel_read.py.j2 │ │ │ │ │ └── channel_write.py.j2 │ │ │ │ ├── claude_generator_config.yml.j2 │ │ │ │ ├── config.yml.j2 │ │ │ │ ├── context_classes.py.j2 │ │ │ │ ├── data │ │ │ │ │ ├── README.md │ │ │ │ │ ├── benchmarks │ │ │ │ │ │ └── datasets │ │ │ │ │ │ │ ├── hierarchical_benchmark.json │ │ │ │ │ │ │ └── in_context_main.json │ │ │ │ │ ├── channel_databases │ │ │ │ │ │ ├── TEMPLATE_EXAMPLE.json │ │ │ │ │ │ ├── examples │ │ │ │ │ │ │ ├── README.md │ │ │ │ │ │ │ ├── consecutive_instances.json │ │ │ │ │ │ │ ├── hierarchical_jlab_style.json │ │ │ │ │ │ │ ├── hierarchical_legacy.json │ │ │ │ │ │ │ ├── instance_first.json │ │ │ │ │ │ │ ├── mixed_hierarchy.json │ │ │ │ │ │ │ └── optional_levels.json │ │ │ │ │ │ ├── hierarchical.json │ │ │ │ │ │ └── in_context.json │ │ │ │ │ ├── channel_limits.json.j2 │ │ │ │ │ ├── raw │ │ │ │ │ │ ├── CSV_EXAMPLE.csv │ │ │ │ │ │ └── address_list.csv │ │ │ │ │ └── tools │ │ │ │ │ │ ├── README.md │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ ├── build_channel_database.py.j2 │ │ │ │ │ │ ├── llm_channel_namer.py.j2 │ │ │ │ │ │ ├── preview_database.py.j2 │ │ │ │ │ │ └── validate_database.py.j2 │ │ │ │ ├── env.example │ │ │ │ ├── framework_prompts │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── python.py.j2 │ │ │ │ │ └── task_extraction.py.j2 │ │ │ │ ├── registry.py.j2 │ │ │ │ ├── requirements.txt.j2 │ │ │ │ └── services │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── channel_finder │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── benchmarks │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── cli.py.j2 │ │ │ │ │ ├── models.py │ │ │ │ │ └── runner.py.j2 │ │ │ │ │ ├── cli.py.j2 │ │ │ │ │ ├── core │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── base_database.py │ │ │ │ │ ├── base_pipeline.py │ │ │ │ │ ├── exceptions.py │ │ │ │ │ └── models.py │ │ │ │ │ ├── databases │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── flat.py │ │ │ │ │ ├── hierarchical.py │ │ │ │ │ └── template.py │ │ │ │ │ ├── examples │ │ │ │ │ ├── custom_database_example.py │ │ │ │ │ └── custom_pipeline_example.py │ │ │ │ │ ├── llm │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── completion.py │ │ │ │ │ ├── pipelines │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── hierarchical │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ ├── models.py │ │ │ │ │ │ └── pipeline.py │ │ │ │ │ └── in_context │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ └── pipeline.py │ │ │ │ │ ├── prompts │ │ │ │ │ ├── hierarchical │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ ├── hierarchical_context.py │ │ │ │ │ │ ├── query_splitter.py │ │ │ │ │ │ └── system.py │ │ │ │ │ └── in_context │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ ├── channel_matcher.py │ │ │ │ │ │ ├── correction.py │ │ │ │ │ │ ├── query_splitter.py │ │ │ │ │ │ └── system.py │ │ │ │ │ ├── service.py │ │ │ │ │ └── utils │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── config.py │ │ │ │ │ └── prompt_loader.py │ │ │ ├── hello_world_weather │ │ │ │ ├── README.md.j2 │ │ │ │ ├── __init__.py │ │ │ │ ├── capabilities │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── current_weather.py.j2 │ │ │ │ ├── context_classes.py.j2 │ │ │ │ ├── framework_prompts.py.j2 │ │ │ │ ├── mock_weather_api.py │ │ │ │ └── registry.py.j2 │ │ │ └── minimal │ │ │ │ ├── INTEGRATION_GUIDE.md │ │ │ │ ├── README.md.j2 │ │ │ │ ├── __init__.py │ │ │ │ ├── capabilities │ │ │ │ ├── __init__.py │ │ │ │ └── example_capability.py.j2 │ │ │ │ ├── context_classes.py.j2 │ │ │ │ └── registry.py.j2 │ │ ├── data │ │ │ ├── __init__.py │ │ │ └── facility_presets.py │ │ ├── project │ │ │ ├── README.md.j2 │ │ │ ├── config.yml.j2 │ │ │ ├── env.example.j2 │ │ │ ├── env.j2 │ │ │ ├── gitignore │ │ │ ├── pyproject.toml.j2 │ │ │ └── requirements.txt │ │ └── services │ │ │ ├── docker-compose.yml.j2 │ │ │ ├── jupyter │ │ │ ├── Dockerfile │ │ │ ├── custom_start.sh │ │ │ ├── docker-compose.yml.j2 │ │ │ ├── python3-epics-readonly │ │ │ │ └── kernel.json.j2 │ │ │ ├── python3-epics-write │ │ │ │ └── kernel.json.j2 │ │ │ └── startup_script.py │ │ │ ├── open-webui │ │ │ ├── ALS_assistant_logo.png │ │ │ ├── Dockerfile │ │ │ ├── custom.css │ │ │ ├── docker-compose.yml.j2 │ │ │ └── functions │ │ │ │ ├── agent_context_button.py │ │ │ │ ├── execution_history_button.py │ │ │ │ ├── execution_plan_editor.py │ │ │ │ ├── memory_button.py │ │ │ │ └── shared │ │ │ │ └── execution_plan_viewer.js │ │ │ └── pipelines │ │ │ ├── __init__.py │ │ │ ├── docker-compose.yml.j2 │ │ │ ├── main.py │ │ │ └── start.sh │ └── utils │ │ ├── __init__.py │ │ ├── config.py │ │ ├── log_filter.py │ │ ├── logger.py │ │ └── streaming.py └── setup.py └── tests ├── __init__.py ├── base ├── __init__.py └── test_capability_helpers.py ├── capabilities ├── __init__.py ├── conftest.py ├── test_channel_write_safety.py ├── test_memory_capability.py ├── test_python_capability.py └── test_time_range_parsing_capability.py ├── cassettes └── README.md ├── cli ├── __init__.py ├── test_claude_config_generation.py ├── test_registry_reset.py └── test_templates.py ├── config ├── __init__.py └── test_config_builder.py ├── conftest.py ├── connectors ├── __init__.py ├── test_auto_verification.py ├── test_connector_factory.py ├── test_mock_connector.py ├── test_pattern_detection.py └── test_write_verification.py ├── context ├── __init__.py └── test_context_manager.py ├── deployment ├── __init__.py ├── test_container_status.py └── test_runtime_helper.py ├── e2e ├── README.md ├── __init__.py ├── conftest.py ├── judge.py ├── test_channel_finder_benchmarks.py ├── test_code_generator_workflows.py ├── test_mcp_capability_generation.py ├── test_runtime_utilities.py └── test_tutorials.py ├── generators ├── __init__.py ├── test_config_updater.py ├── test_config_updater_control_system.py ├── test_config_updater_epics.py └── test_registry_updater.py ├── infrastructure ├── __init__.py ├── conftest.py ├── test_gateway_approval.py ├── test_gateway_approval_integration.py ├── test_infrastructure_decorator.py └── test_router_node.py ├── integration ├── __init__.py └── test_e2e_workflow.py ├── prompts ├── __init__.py └── test_clarification_prompt.py ├── registry ├── __init__.py ├── test_provider_registration.py ├── test_registry_helpers.py ├── test_registry_isolation.py ├── test_registry_loading.py ├── test_registry_modes.py └── test_registry_validation.py ├── runtime ├── __init__.py ├── test_runtime.py └── test_runtime_integration.py ├── services ├── __init__.py ├── channel_finder │ ├── test_all_example_databases.py │ ├── test_example_databases.py │ ├── test_hierarchical_flexible.py │ ├── test_hierarchical_optional_levels.py │ ├── test_hierarchical_separator_override.py │ ├── test_hierarchy_traversal.py │ ├── test_preview_database.py │ └── test_registration.py └── python_executor │ ├── README_MOCK_GENERATOR.md │ ├── __init__.py │ ├── conftest.py │ ├── execution │ └── test_limits_validator.py │ ├── test_claude_code_generator.py │ ├── test_generator_interface.py │ ├── test_limits_integration.py │ ├── test_mock_generator.py │ ├── test_pattern_detection_integration.py │ ├── test_result_validation.py │ ├── test_result_validation_integration.py │ ├── test_runtime_limits_e2e.py │ ├── test_service_integration.py │ └── test_state_reducers.py ├── templates ├── control_assistant │ └── test_task_extraction_prompt.py └── data │ └── test_facility_presets.py └── utils ├── __init__.py ├── test_log_filter.py └── test_logger.py /.github/pull_request_template.md: 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