src/
├── dna/ # Core DNA modules containing main compiler components
│ ├── atp/ # Abstract syntax tree processing and language parsing
│ │ ├── ast.rs # Abstract syntax tree node definitions and structures
│ │ ├── interpreter.rs # AST interpretation and execution engine
│ │ ├── lexer.rs # Tokenization and lexical analysis
│ │ ├── mod.rs # Module exports for ATP components
│ │ ├── ops.rs # Operator parsing and processing
│ │ ├── output.rs # AST output formatting and serialization
│ │ ├── parser.rs # Grammar parsing and AST construction
│ │ ├── types.rs # Core type definitions and data structures
│ │ ├── value.rs # Value representation and manipulation
│ │ └── verify.rs # AST validation and verification
│ ├── bch/ # Benchmarking and performance testing utilities
│ │ ├── mod.rs # Benchmark module exports
│ │ └── parser_bench.rs # Parser performance benchmarking
│ ├── bin/ # Binary executables and test utilities
│ │ ├── helix.rs # Main Helix binary entry point
│ │ └── test-utils/ # Test utility functions
│ │ ├── create_binaries.rs # Binary creation utilities
│ │ └── test_edge_cases.rs # Edge case testing utilities
│ ├── cmd/ # CLI command implementations for hlx tool
│ │ ├── add.rs # Add command implementation
│ │ ├── a_example.rs # Example command template
│ │ ├── bench.rs # Benchmark command
│ │ ├── binary.rs # Binary management command
│ │ ├── build.rs # Build command with optimization
│ │ ├── bundle.rs # Bundle creation command
│ │ ├── cache.rs # Cache management command
│ │ ├── clean.rs # Cleanup command
│ │ ├── compile.rs # Compilation command
│ │ ├── completions.rs # Shell completion generation
│ │ ├── config.rs # Configuration management
│ │ ├── dataset.rs # Dataset handling command
│ │ ├── decompile.rs # Decompilation command
│ │ ├── diagnostics.rs # Diagnostic information command
│ │ ├── diff.rs # File difference comparison
│ │ ├── doctor.rs # System health check command
│ │ ├── export.rs # Export functionality
│ │ ├── filter.rs # Data filtering command
│ │ ├── fmt.rs # Code formatting command
│ │ ├── generate.rs # Code generation command
│ │ ├── import.rs # Import functionality
│ │ ├── info.rs # Information display command
│ │ ├── init.rs # Project initialization command
│ │ ├── json.rs # JSON processing command
│ │ ├── lint.rs # Code linting command
│ │ ├── loader.rs # File loading utilities
│ │ ├── migrate.rs # Migration command
│ │ ├── mod.rs # Command module exports
│ │ ├── optimizer.rs # Optimization command
│ │ ├── preview.rs # Preview functionality
│ │ ├── project.rs # Project management
│ │ ├── publish.rs # Publishing command
│ │ ├── reset.rs # Reset command
│ │ ├── rm.rs # Remove command
│ │ ├── runtime.rs # Runtime management
│ │ ├── schema.rs # Schema validation
│ │ ├── search.rs # Search functionality
│ │ ├── serializer.rs # Serialization utilities
│ │ ├── serve.rs # Server command
│ │ ├── sign.rs # Code signing command
│ │ ├── templates.rs # Template management
│ │ ├── test.rs # Testing command
│ │ ├── tools.rs # Development tools
│ │ ├── validate.rs # Validation command
│ │ ├── watch.rs # File watching command
│ │ └── workflow.rs # Workflow management
│ ├── exp/ # Experimental features and parsing experiments
│ │ ├── basic_parsing.rs # Basic parsing experiments
│ │ ├── hlx_format copy.rs # HLX format experiments
│ │ └── mod.rs # Experimental module exports
│ ├── ffi/ # Foreign function interface bindings for other languages
│ │ ├── csharp.rs # C# language bindings
│ │ └── mod.rs # FFI module exports
│ ├── hel/ # Core Helix language runtime and error handling
│ │ ├── dispatch.rs # Command dispatch system
│ │ ├── dna_hlx.rs # DNA-Helix integration
│ │ ├── error.rs # Error handling and types
│ │ ├── hlx.rs # Core Helix functionality
│ │ ├── integration.rs # System integration
│ │ └── mod.rs # Helix core module exports
│ ├── json/ # JSON processing and metadata handling
│ │ ├── caption.rs # JSON caption handling
│ │ ├── concat.rs # JSON concatenation
│ │ ├── core.rs # Core JSON processing
│ │ ├── hf.rs # HuggingFace JSON format
│ │ ├── metadata.rs # JSON metadata handling
│ │ ├── mod.rs # JSON module exports
│ │ ├── reasoning.rs # JSON reasoning logic
│ │ └── st.rs # JSON string templates
│ ├── mds/ # Multi-domain system implementations and optimizations
│ │ ├── add.rs # MDS add functionality
│ │ ├── a_example.rs # MDS example template
│ │ ├── benches.rs # MDS benchmarking
│ │ ├── bench.rs # MDS benchmark command
│ │ ├── binary.rs # MDS binary handling
│ │ ├── build.rs # MDS build system
│ │ ├── bundle copy.rs # MDS bundle backup
│ │ ├── bundle.rs # MDS bundle creation
│ │ ├── cache.rs # MDS cache management
│ │ ├── clean.rs # MDS cleanup
│ │ ├── codegen.rs # MDS code generation
│ │ ├── compile.rs # MDS compilation
│ │ ├── completions.rs # MDS completions
│ │ ├── config.rs # MDS configuration
│ │ ├── dataset.rs # MDS dataset handling
│ │ ├── decompile.rs # MDS decompilation
│ │ ├── diagnostics.rs # MDS diagnostics
│ │ ├── diff.rs # MDS diff functionality
│ │ ├── doctor.rs # MDS health checks
│ │ ├── export.rs # MDS export
│ │ ├── filter.rs # MDS filtering
│ │ ├── fmt.rs # MDS formatting
│ │ ├── generate.rs # MDS generation
│ │ ├── import.rs # MDS import
│ │ ├── info.rs # MDS information
│ │ ├── init.rs # MDS initialization
│ │ ├── json.rs # MDS JSON processing
│ │ ├── lint.rs # MDS linting
│ │ ├── loader.rs # MDS loading
│ │ ├── migrate.rs # MDS migration
│ │ ├── mod.rs # MDS module exports
│ │ ├── optimizer.rs # MDS optimization
│ │ ├── preview.rs # MDS preview
│ │ ├── project.rs # MDS project management
│ │ ├── publish.rs # MDS publishing
│ │ ├── reset.rs # MDS reset
│ │ ├── rm.rs # MDS removal
│ │ ├── run.rs # MDS execution
│ │ ├── runtime.rs # MDS runtime
│ │ ├── schema.rs # MDS schema
│ │ ├── search.rs # MDS search
│ │ ├── semantic.rs # MDS semantic analysis
│ │ ├── serializer.rs # MDS serialization
│ │ ├── server.rs # MDS server
│ │ ├── serve.rs # MDS serving
│ │ ├── sign.rs # MDS signing
│ │ ├── templates.rs # MDS templates
│ │ ├── test copy.rs # MDS test backup
│ │ ├── test.rs # MDS testing
│ │ ├── tools.rs # MDS tools
│ │ ├── validate.rs # MDS validation
│ │ ├── watch copy.rs # MDS watch backup
│ │ ├── watch.rs # MDS file watching
│ │ └── workflow.rs # MDS workflow
│ ├── mod.rs # DNA module exports
│ ├── ngs/ # Next-generation system integrations
│ │ ├── mod.rs # NGS module exports
│ │ └── python.rs # Python integration
│ ├── ops/ # Operator implementations and execution engine
│ │ ├── conditional.rs # Conditional operations
│ │ ├── eval.rs # Expression evaluation
│ │ ├── fundamental.rs # Core @-prefixed operators
│ │ ├── math.rs # Mathematical operations
│ │ ├── mod.rs # Operations module exports
│ │ ├── parser.rs # Operation parsing
│ │ ├── string_processing.rs # String manipulation
│ │ ├── ulator.pest # Pest grammar file
│ │ └── validation.rs # Input validation
│ ├── out/ # Output format generators and serializers
│ │ ├── helix_format.rs # Helix format output
│ │ ├── hlxb_config_format.rs # HLXB config format
│ │ ├── hlxc_format.rs # HLXC format output
│ │ ├── hlx_config_format.rs # HLX config format
│ │ └── mod.rs # Output module exports
│ └── tst/ # Test suites and integration testing
│ ├── calculator_integration_tests.rs # Calculator integration tests
│ ├── debug_parse.rs # Parse debugging utilities
│ ├── debug_semantic.rs # Semantic debugging
│ ├── e621_tests.rs # E621 API tests
│ ├── forge_integration_demo.rs # Forge integration demo
│ ├── fundamental_ops.rs # Fundamental operations tests
│ ├── hlxc_try.rs # HLXC testing
│ ├── hlx_integration_tests.rs # HLX integration tests
│ ├── integration_tests.rs # General integration tests
│ ├── load.rs # Loading tests
│ ├── mod.rs # Test module exports
│ ├── test_binary_loading.rs # Binary loading tests
│ ├── test_duration_space.rs # Duration space tests
│ ├── test_lexer_fixes.rs # Lexer fix tests
│ ├── tests-b/ # Backup test directory
│ │ ├── debug_parse.rs # Parse debugging backup
│ │ ├── debug_semantic.rs # Semantic debugging backup
│ │ ├── forge_integration_demo.rs # Forge integration backup
│ │ ├── integration_tests.rs # Integration tests backup
│ │ ├── mod.rs # Test backup module exports
│ │ └── test_binary_loading.rs # Binary loading tests backup
│ ├── tests.rs # General test suite
│ ├── text_tests.rs # Text processing tests
│ └── t-r-y-h-l-x.rs # Try HLX tests
├── hlx.rs # Main Helix binary
├── lib.rs # Library root and exports
└── src_tree.txt # Source tree documentation