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  # Level 1: Quick Start (Entry Point)
  - Start Here:
      - 15-Minute Quickstart: 01-getting-started/quickstart_15min.md
      - Installation: 01-getting-started/installation.md
      - Getting Started: 01-getting-started/getting_started.md
      - Quickstart (CLI): 01-getting-started/quickstart_cli.md
      - Quickstart (Python): 01-getting-started/quickstart_python.md
      - Quickstart (Protocol): 01-getting-started/quickstart_protocol.md
      - First Steps (CLI): 01-getting-started/first-steps_cli.md
      - FAQ (Basic): 01-getting-started/faq_basic.md

  # Level 2: Foundations (Conceptual Basis)
  - Foundations:
      - Introduction: index.md
      - Spectroscopy Fundamentals: 07-theory-and-background/spectroscopy_basics.md
      - Food Spectroscopy Applications: 05-advanced-topics/hsi_and_harmonization.md
      - Scope & Limitations: non_goals_and_limitations.md
      - Domain Overview: 07-theory-and-background/domains_overview.md

  # Level 3: Theory & Methods (Scientific Underpinnings)
  - Theory & Background:
      - Spectroscopy Theory: 07-theory-and-background/spectroscopy_basics.md
      - Chemometrics & ML Basics: 07-theory-and-background/chemometrics_and_ml_basics.md
      - RQ Engine Theory: 07-theory-and-background/rq_engine_detailed.md
      - Harmonization Theory: 07-theory-and-background/harmonization_theory.md
      - Validation Theory: 05-advanced-topics/validation_strategies.md
      - Model Lifecycle: 05-advanced-topics/model_lifecycle.md
      - MOATS Overview: 07-theory-and-background/moats_overview.md

  # Level 4: Methods & Preprocessing (Practical Implementation)
  - Methods & Preprocessing:
      - Overview: 03-cookbook/cookbook_intro.md
      - Preprocessing Recipes: 03-cookbook/preprocessing_guide.md
      - Chemometrics Guide: 03-cookbook/chemometrics_guide.md
      - FTIR/Raman Methods: 03-cookbook/ftir_raman_preprocessing.md
      - RQ Features Guide: 03-cookbook/cookbook_rq_questions.md
      - Data Formats & HDF5: 04-user-guide/data_formats_and_hdf5.md
      - Registry & Plugins: 04-user-guide/registry_and_plugins.md

  # Level 5: Modeling & Validation (ML & Statistics)
  - Modeling & Statistics:
      - Overview: 05-advanced-topics/architecture.md
      - Model Architecture: 05-advanced-topics/design_overview.md
      - Model Lifecycle & Prediction: 05-advanced-topics/model_lifecycle.md
      - Model Registry: 05-advanced-topics/model_registry.md
      - Validation Strategies: 05-advanced-topics/validation_strategies.md
      - MOATS Implementation: 05-advanced-topics/MOATS_IMPLEMENTATION.md
      - Validation Recipes: 03-cookbook/cookbook_validation.md
      - Baseline Validation: 03-cookbook/validation_baseline.md
      - Chemometrics (Oils): 03-cookbook/validation_chemometrics_oils.md
      - Peak Ratios: 03-cookbook/validation_peak_ratios.md

  # Level 6: Applications & Workflows (Domain Expertise)
  - Applications:
      - Oil Authentication: workflows/oil_authentication.md
      - Heating Quality: workflows/heating_quality_monitoring.md
      - Mixture Analysis: workflows/mixture_analysis.md
      - Batch QC: workflows/batch_quality_control.md
      - Hyperspectral Mapping: workflows/hyperspectral_mapping.md
      - Custom Workflows: workflows/workflow_design_and_reporting.md
      - Aging Workflows: workflows/aging_workflows.md
      - Harmonization & Calibration: workflows/harmonization_automated_calibration.md
      - Multimodal Workflows: 05-advanced-topics/multimodal_workflows.md

  # Level 7: Tutorials & Learning (Step-by-Step)
  - Tutorials:
      - Beginner:
          - Oil Discrimination (Basic): 02-tutorials/oil_discrimination_basic.md
          - Reference Analysis: 02-tutorials/reference_analysis_oil_authentication.md
          - Raman GUI Quickstart: 02-tutorials/raman_gui_quickstart.md
      - Intermediate:
          - Matrix Effects: 02-tutorials/oil_vs_chips_matrix_effects.md
          - Thermal Stability: 02-tutorials/thermal_stability_tracking.md
          - GUI Workflow: 02-tutorials/modeling_gui_foodspec_workflow.md
      - Advanced:
          - HSI Surface Mapping: 02-tutorials/hsi_surface_mapping.md
          - End-to-End Notebooks: 02-tutorials/end_to_end_notebooks.md
          - Advanced Deep Learning: 05-advanced-topics/advanced_deep_learning.md
      - Example Catalog: 06-tutorials/example_catalog.md

  # Level 8: Protocols & Reproducibility (Publication Support)
  - Protocols:
      - Protocols Overview: protocols/protocols_overview.md
      - Reference Protocol: protocols/reference_protocol.md
      - Methods Text Generator: protocols/methods_text_generator.md
      - Protocol Cookbook: 03-cookbook/protocol_cookbook.md
      - Protocol Benchmarks: protocols/protocol_benchmarks.md
      - Statistical Power & Design: protocols/statistical_power_and_limits.md

  # Level 9: User Guide (Operations & Configuration)
  - User Guide:
      - CLI Guide: 04-user-guide/cli.md
      - CLI Help Reference: 04-user-guide/cli_help.md
      - Protocols & YAML: 04-user-guide/protocols_and_yaml.md
      - Automated Analysis: 04-user-guide/automation.md
      - Protocol Profiles: 04-user-guide/protocol_profiles.md
      - Logging & Configuration: 04-user-guide/config_logging.md
      - Data Governance: 04-user-guide/data_governance.md
      - Library Management: 04-user-guide/libraries.md
      - Library Search: 04-user-guide/library_search.md
      - CSV to Library: 04-user-guide/csv_to_library.md
      - Vendor I/O: 04-user-guide/vendor_io.md
      - Registry & Reporting: 03-cookbook/cookbook_registry_reporting.md
      - Troubleshooting: 03-cookbook/cookbook_troubleshooting.md
      - Troubleshooting FAQ: troubleshooting/troubleshooting_faq.md
      - Reporting Guidelines: troubleshooting/reporting_guidelines.md

  # Level 10: API Reference (Code Documentation)
  - API Reference:
      - Overview: 08-api/index.md
      - Core API: 08-api/core.md
      - Machine Learning: 08-api/ml.md
      - Statistics: 08-api/stats.md

  # Level 11: Reference Materials (Supporting Documentation)
  - Reference:
      - Metric Significance Tables: 09-reference/metric_significance_tables.md
      - Glossary: 09-reference/glossary.md
      - Keyword Index: 09-reference/keyword_index.md
      - Method Comparison: 09-reference/method_comparison.md
      - ML Model VIP Scores: 09-reference/ml_model_vip_scores.md
      - Non-Goals & Limitations: non_goals_and_limitations.md
      - Changelog: 09-reference/changelog.md
      - Citing FoodSpec: 09-reference/citing.md
      - Versioning: 09-reference/versioning.md
      - Archive (Historical): archive/README.md

  # Level 12: Developer Guide (Extension & Contribution)
  - Developer Guide:
      - Contributing: 06-developer-guide/contributing.md
      - Testing & CI: 06-developer-guide/testing_and_ci.md
      - Testing Coverage: 06-developer-guide/testing_coverage.md
      - Architecture: 05-advanced-topics/architecture.md
      - Integration Checklist: 06-developer-guide/integration_checklist.md
      - Documentation Guidelines: 06-developer-guide/documentation_guidelines.md
      - Extending Protocols: 06-developer-guide/extending_protocols_and_steps.md
      - Writing Plugins: 06-developer-guide/writing_plugins.md
      - Deployment Artifacts: 05-advanced-topics/deployment_artifact_versioning.md
      - HDF5 Schema Versioning: 05-advanced-topics/deployment_hdf5_schema_versioning.md
      - Releasing: 06-developer-guide/releasing.md
      - Release Checklist: 06-developer-guide/RELEASE_CHECKLIST.md

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