Introduction | Overview: Why Centralised Bibliography Management? | Setting Up Bibliography Management | Step 1: Configure Your Bibliography Source | Step 2: Download and Cache the Bibliography | Step 3: Copy Bibliography to Your Project | Validating References | Verify All Citations Exist | Handle Missing References | Integration with Document Generation | Automatic Bibliography Distribution | Quarto/R Markdown Integration | Advanced Workflows | Project-Specific Bibliography Subsets | Multi-Author Collaboration | Automated Reference Verification | Best Practices | 1. Maintain a Central Bibliography | 2. Cache Management | 3. Citation Key Conventions | Troubleshooting | Common Issues and Solutions | Bibliography Not Downloading | Cache Issues | Validation Errors | Complete Example Workflow | Summary

Overview | Core Architecture Components | 1. Unified Database System | Key Design Principles | 2. Path System | Path Operations | 3. Template Variable System | Variable Scoping | 4. File Organisation | Data Flow Architecture | 1. Initialisation Flow | 2. Import Flow | 3. Text Generation Flow | Key Design Patterns | 1. Function Naming Convention | 2. Error Handling Strategy | 3. Extensibility Points | Adding New Categories | Adding New Formats | 4. Performance Considerations | Database Schema | Unified Database Structure | Entry Types | Text Entries (methods, results, discussion) | Measure Entries | Testing Architecture | Test Organisation | Testing Strategy | Security Considerations | Future Architecture Considerations | Planned Enhancements | Backwards Compatibility

Introduction | Scenario: Writing a Psychology Manuscript | Step 1: Initial Project Setup | Install and Load the Package | Create Project Structure | Step 2: Explore the Default Content | View Available Methods | View Available Measures | Step 3: Customise for Your Study | Add Study-Specific Methods | Add Study-Specific Measures | Step 4: Set Up Bibliography Management | Step 5: Generate Your Methods Section | Define Study Parameters | Generate Complete Methods Section | Step 6: Generate Measures Section | Generate output for political orientation if we added it | Step 7: Validate Your Work | Verify Database Structure | Verify References | Export for Version Control | Step 8: Create Your Manuscript | Quarto Document Example | Measures | Results | Discussion | 2. Multiple Manuscripts from Same Dataset | 3. Batch Updates | 4. Quality Control | Summary | Next Steps

Introduction | Core Database Operations | Database Structure Navigation | get_nested_folder() | modify_nested_entry() | Database Utilities | sort_db_recursive() | merge_recursive_lists() | Template System | apply_template_vars() | File I/O Operations | get_db_file_path() | read_boilerplate_db() | write_boilerplate_db() | Default Databases | get_default_db() | Category-specific getters | JSON Support Functions | standardise_json_structure() | clean_for_json() | Bibliography Support | parse_bibtex_keys() | extract_citation_keys() | Migration Utilities | detect_database_type() | migrate_to_unified_json() | Measures-Specific Functions | transform_label() | Best Practices for Using Internal Functions | Contributing New Internal Functions

Overview | Key Features | Quick Start | 1. Initialise Databases | 2. Import Databases | 3. Generate Text | 4. Generate Measure Descriptions | Working with Databases | Viewing Database Content | Adding and Updating Content | Batch Operations | Template System | Best Practices | Advanced Features | Measure Standardisation | Cross-Project Workflows | Managing Database Versions | Listing Available Versions | Working with Timestamped Versions | Backup and Restore | Getting Help

Why Boilerplate? | Real-World Example: A Multi-Study Project | Setting Up the Project | Creating Reusable Methods Components | Study 1: Pilot Study | Study 2: Main Study | Managing Measures Across Studies | Creating a Measure Library | Generating Consistent Measure Descriptions | Collaborative Features | Sharing Across Team Members | Batch Updates | Advanced Workflows | Dynamic Report Generation | Quality Control | Integration with R Markdown/Quarto | Document Generation | Best Practices | 1. Organize Your Content Hierarchically | 2. Use Meaningful Variable Names | 3. Version Control Your Boilerplate | 4. Create Project-Specific Templates | Summary

Overview | Unified Database Schema | Methods Database Schema | Basic Structure | Entry Variants | Fields | Measures Database Schema | Complete Example | Required Fields | Optional Fields | For All Types | For Categorical/Ordinal | For Continuous | For Scales | Results Database Schema | Template Database Schema | Variable Scoping | Schema Validation | JSON Schema Files | Validation in R | Common Validation Errors | Migration from RDS | Converting RDS to JSON | Format Differences | JSON Format (default) | RDS Format (not written by package APIs) | Handling Special Cases | Best Practices | File Organisation | Naming Conventions | Version Control | Performance Considerations | Examples | Creating a New Measures Entry | Adding a Methods Entry with Variants | Template Variables with Overrides

Introduction | Project Basics | Default Project | Creating a New Project | Working with Projects | Project Organization | Cross-Project Operations | Listing Projects | Copying Between Projects | Conflict Handling | Practical Workflow Example | Best Practices | Migration from Pre-1.1.0 | Summary

Introduction | Why Use boilerplate with Quarto? | Setting Up a Quarto Project | Recommended Project Structure | Initialise boilerplate | Configure .gitignore | Building Your Text Database | Methods Templates | Measures Database | Using Templates in Quarto | Example Quarto Document Structure | Best Practices | Bibliography Management | Automatic Bibliography Copying | Validating Citations | Advanced Features | Batch Updates | Quarto Parameters | Conclusion

Overview | Managing Multiple Versions | Working with Timestamped Versions | Backup and Recovery | Version Management Workflow | Best Practices | Integration with Version Control | Troubleshooting | Finding Lost Work | Recovering from Corruption | Summary

Introduction | Basic JSON Operations | Importing and Saving JSON Databases | Working with Category-Specific JSON Files | Migrating from RDS to JSON | Batch Editing JSON Databases | Standardising Measures in JSON Format | Validating JSON Structure and Health | Schema Validation | Database Validation | Integration with Existing Workflow | Best Practices | Conclusion

Overview | Quick Start: Adding and Using Measures | Basic Workflow | Understanding Measure Structure | Required Fields | Optional Fields | Common Mistakes to Avoid | ❌ Incorrect: Nesting measures under categories | ✅ Correct: Top-level measure entries | Managing Multiple Measures | Adding Multiple Measures at Once | Interactive Management | Standardising Measures | What Standardisation Does | Running Standardisation | Example: Before and After Standardisation | Before: | After standardisation: | Generating Quality Reports | Basic Quality Assessment | Detailed Quality Analysis | Batch Operations on Measures | Finding Entries to Clean | Batch Cleaning | Batch Editing | Generating Formatted Output | Basic Measure Text | Multiple Measures with Categories | Advanced Formatting Options | Complete Workflow Example | Best Practices | 1. Measure Organisation | 2. Quality Control | 3. Workflow Tips | 4. Integration with Text Generation | Troubleshooting | Common Issues | Measure not found | Standardisation warnings | Missing required fields | Getting Help | Summary