feat: Enhance PSD plotting and update GP kernel parameters

- Updated GP kernel parameter names from 'log_gp_lengthscale' to 'log_gp_scale' across various files for consistency.
- Modified reporting functions to include nominal uncertainties and jitter in periodogram plots.
- Improved y-axis scaling logic in periodogram plots to better reflect data characteristics.
- Updated configuration documentation and generator to reflect changes in GP parameters.
- Adjusted tests to align with new parameter naming conventions.