Config refactor#38
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Replace static class configuration with instance-based MalariaConfig to enable thread-safe parallel simulations. Each IntrahostComponent now owns a shared_ptr to its config, including its own RNG and SUID generator. API changes: - Add create_config(params) to create config instances from defaults - Add config.update(params) for incremental parameter updates - IntrahostComponent.create() now requires a config argument - Remove static set_params()/update_params() methods - Add config.yaml property for YAML representation New files: - MalariaConfig.h/cpp: Consolidated configuration class - test_thread_safety.py: Tests for parallel simulation isolation - MIGRATION.md: Migration guide from v0.0.4 to v0.1.0 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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