what is annotating
SDF = Standard Delay Format.
Typically in design flow you flow from architecture, RTL, simulation, synthesis, floor planning, layout design .. just as you mention.
To explain where SDF is generated and whats is use. Let me tk the case of synthesis. As you know after synthesis you get the gate level netlist. Which is nothing but the functional description of you logic in gate level.
But what about the typical, gate delays an wire delays that you have at silicon level. This is not embeded in the netlist. But it is stored differently in different file called "Standard delay format (SDF)". That contains the delays. So typcillay when you do gate level simulation your requrie even SDF to simulate as closely as the simulation in the physical device i.e with delays.
The point is where all do we annotate this SDF, the point is linked with the how accurate is the delay value in the SDF. The dealy values in the SDF are close to real physical delays aftef PnR and layout is done. The SDF extarcted here has more accurate delays.