[akutuva21]

Summary

• Integrate the native C++ backend across parsing, model API compatibility, NFsim routes, scans, sensitivity, CLI, and visualization paths.
• Add parser, network, direct-NF, legacy-format, and validation-harness regression coverage.
• Record parity evidence, known gaps, and reproducible build/test workflows.

Validation

• CTest: 120/120 passed in the latest full gate.
• NF fixed-seed parity gate: 8 passed.
• Focused mixed-scope local-observable NF regression: passed.
• Deterministic model validation: 40 passed, 0 failed, 1 explicit SBML atomizer-path error, 30 skipped.

Known limitations

• SBML atomization remains an explicit unsupported conversion path.
• Some legacy/native fixtures are stale or use unsupported nested dynamic local-function semantics; these remain documented rather than silently approximated.

This branch contains the requested implementation plan and its incremental commits.

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