- Replace direct array access with SymbolRepository for functions, classes, interfaces
- Introduce DiagnosticReporter interface with CLI and throwing implementations
- Add NativeBuilder for compile/link command management and parallel processing
- Create CommandOptions base class for compile and link options handling
- Implement project YAML loader with PHP version and OS family conditions
- Remove old array properties and update all related method calls
- Update compiler diagnostic methods to use new reporter pattern
- Refactor native compilation to use builder pattern with proper options
- Modify test utilities to work with new symbol repository structure
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