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Fixed
nlsq_result.npz now carries c2_exp/c2_fitted/residuals/t1/t2/phi_angles/wavevector_q. save_results_npz previously wrote only scalars, parameters, and
covariance — the raw (n_phi, n_t1, n_t2) correlation surfaces (and the
scattering wavevector needed to interpret them) a user needs for
downstream re-analysis were only ever written to plots/simulated_data/c2_fitted_data.npz, and only when plotting was
enabled. service/persist.py::merge_fitted_c2() now folds those
already-computed arrays into the primary NPZ (best-effort, mtime-guarded
against stale leftovers from a previous run in the same output directory)
after plotting runs, for both the CLI and the GUI worker.
Whole-codebase module-review sweep: 18 findings fixed across 12 modules
(2 confirmed HIGH blockers + 16 advisory). Highlights: ParameterSpace.from_config
crashed on a blank parameter_space: YAML section; public xpcsjax.HeterodyneModel
resolved to the no-arg PhysicsModelBase adapter instead of the documented
stateful model used by every production heterodyne path and the test suite.
Advisory fixes span CLI persistence logging, config parameter-name aliasing,
path-traversal-check de-duplication, an OOM-risk unbounded residuals scatter
plot, and more.