The "Warranty efficiency curve" of most PV module's manufacturers show a warranty beginning with 97 or 98% guaranteed efficiency for the first year.
In PVsyst, for one module this initial performance loss is mainly represented by the LID losses, which take place within the first hours of exposure of the PV modules to the sun.
There may also be a contribution of the Power tolerance, or even for taking the Flash-test accuracy (not better than 2-3%) into account. Please ask the manufacturer for this interpretation.
The LID loss is applied to any simulation, for any year: the PV modules are "damaged" at the beginning, and stay like this all over the system's life.
Parameters of the Ageing Tool
Please note that the manufacturer's curve gives a Warranty for one module. It doesn't mean that the degradation of all modules will behave in this way.
The average degradation for the whole system (average of the modules) will probably be much lower (this was reported as about -0.3% to -0.4%/year, by the very few studies about long-term degradation, and for very old modules).
As all the modules will not degrade in the same way, the degradation loss will also be affected by the increasing mismatch between modules along years, which you can model in this tool, using a Monte-Carlo stochastic method.
Simulation without specifying an ageing degradation: this "usual" simulation will represent the system's state at the commissioning time. It includes the initial LID loss.
Simulation with ageing, for the first year of operation: this will also include the specified initial LID loss. If you specify a degradation rate of, say, 0.4%/year, then at the beginning of the year the degradation will be null, and at the end it will be 0.4%, therefore an average of 0.2% for the global simulation of the first year.
The tool "Degradation" in the detailed losses gives the opportunity of performing the simulation for any given year after commissioning.
In the "Detailed Simulation" option, you can perform a simulation over all (or several chosen) years, in order to get a summary of the yield of your system along its lifetime.