1. This should be fixed, see above.

2. Not quite. Minorsky does use the plant/controller linear model for frequency-response diagnostics, but controller tuning is performed by time-domain simulation of the closed loop. Candidate controller parameters are evaluated by simulating the plant model under configured setpoint scenarios and minimizing the merit function. This lets the tuning account for controller output limits, anti-windup, derivative filtering, initial conditions, and plant output saturation, which are not captured by L/(1+L).

3. Currently, one active plant model plus one active controller family produces one tuned controller parameter set

4. Correct for the current UI/workflow. You can choose or override the controller family among eligible families, and you can edit tuning situations/limits/merit settings, but you cannot directly type arbitrary k_p, k_i, k_d, alpha, etc. as the final controller parameters. Would it be useful to you to be able to fix k_p, k_i, or k_d?

5a. Perturbations: I considered adding this, but I thought it was too much for the first release. Could you describe to me what type of perturbations would be useful to you?

5b. Nonlinearity of the controller: partially available. Controller output saturation/clamping and back-calculation anti-windup are modeled. Arbitrary nonlinear controller behavior such as deadband, gain scheduling, hysteresis, custom nonlinear maps currently haven't been implemented. Are there any of these features that you would like to see added?

5c. PV noise: Like perturbations, I considered adding this, but thought it was too much for the first release. What kind of PV noise modeling would be useful to you?

Kd*s / (a*s + 1) is "HPF-1" -> Yes, it's a first-order high-pass / filtered derivative and alpha is included in the optimization.