Add scope resolution, AST serialization, and test improvements

[revarbat]

Summary

• Adds lexical scope building with three separate namespaces (variables, functions, modules) via ast/scope.py
• Adds JSON/YAML AST serialization/deserialization via ast/serialization.py
• Adds parser_comments fixture to conftest and uses it in test_modules
• Moves pytest-cov to dev dependencies (was incorrectly in main dependencies)
• Updates PRD.md to reflect v2.2.0+ capabilities

Test plan

• pytest tests/ passes (599 passed, 3 skipped)
• pytest-cov available in dev installs but not as a runtime dependency

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