Repository Structure

The codebase is organized as a MATLAB package (+HERA) to ensure namespace isolation.

HERA-Matlab/
├── +HERA/                         % Main Package Namespace
│   ├── +output/                   % Report Generation (PDF, JSON, CSV)
│   ├── +analysis/                 % Scientific Analysis Modules
│   │   └── convergence_analysis.m % Robust Convergence Verification
│   ├── +plot/                     % Visualization (Sankey, Heatmaps)
│   ├── +run/                      % Execution Logic
│   ├── +start/                    % CLI & Configuration Logic
│   ├── +stats/                    % Statistical Core (Cliff's Delta, Convergence Check)
│   ├── +test/                     % Unit Test Suite
│   ├── language/                  % Localization Files
│   ├── bootstrap_ranking.m        % Cluster Bootstrap Analysis
│   ├── borda_ranking.m            % Consensus Ranking
│   ├── calculate_bca_ci.m         % BCa Confidence Intervals
│   ├── calculate_ranking.m        % Core Ranking Logic
│   ├── calculate_thresholds.m     % Threshold Calculation
│   ├── Contents.m                 % Toolbox Documentation (ver, help)
│   ├── default.m                  % Global Defaults
│   ├── design.m                   % Style & Design Definitions
│   ├── generate_output.m          % Output Generation Controller
│   ├── generate_plots.m           % Plot Generation Controller
│   ├── get_language.m             % Language Loader
│   ├── get_version.m              % Version Retrieval
│   ├── load_data.m                % Data Import & Validation
│   ├── power_analysis.m           % Power Analysis
│   ├── run_ranking.m              % Core Function (Developer API)
│   ├── start_ranking.m            % Main Entry Point (User API)
│   └── run_unit_test.m            % Test Runner
├── assets/                        % Images & Logos
├── data/                          % Data Directory
│   ├── examples/                  % Synthetic Example Datasets
│   └── README.md                  % Data Documentation
├── deploy/                        % Build Scripts (Standalone App)
├── docs/                          % Documentation & Guides
├── paper/                         % Paper Resources
├── tests/                         % Unit Test & Analysis Reports
├── setup_HERA.m                   % Path Setup Script
├── CITATION.cff                   % Citation Metadata
├── CODE_OF_CONDUCT.md             % Community Standards
├── CONTRIBUTING.md                % Contribution Guidelines
├── LICENSE                        % License File
└── README.md                      % Global Documentation