True wind.
FMS always works in true and then at the last minute converts the bits you need to be told into magnetic using local variation before displaying the heading / track to you.
In a very simplistic way - A to B, great circle track - convert to average track, apply wind and hey presto, you have average wind component etc etc.
Try doing the same with magnetic figures when the variation goes from 20E to 20W in random uneven stages along the track.
If you fly EFIS, have a look at the wind readout in numbers in the FMS (true) and then look at the wind arrow on the screen (magnetic). The difference should be the variation. Switch your reference to True and see what happens.
These days aircraft will happily fly all day and night referenced to true north. It is only to please the pilot / atc / current chart publications that magnetic is used.
Even if your company provides you with a PLOG showing only magnetic track, magnetic winds etc etc, the computer will have done the calculation using true. Anything else would be overly complicated.
I think that I made the point earlier - if you upload winds through ACARS / AFIS etc then they will be true winds and your FMS will be happy. You would have to be really bored / have too much pre-flight time to look up the local variation at every winf point and adjust the figure.
