This code contains a few files. wgenerator.m and wfromzernikecoef.m can be largely ignored - they are repository of W functions (W020, W040, etc) and zernike functions that describe pupils.
The machinery is contained in AberrationSwissArmyKnife.m, which requires PupilPerscription.m. The latter, as you may guess, describes the pupil of an optical system mathematically.
A pupil prescription is defined as having a notation ("S," aka Seidel, or "Z," Fringe Zernike).
The fringe zernike polynomials used are not a normalized set, so using e.g. Z8 with magnitude 1 does not produce anything like 1 wave of spherical (either 0 to peak or RMS). The zernike terms can be traced back to combinations of W polynomial expressions and this used to compute appropriate normalizations.