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1) Some Battle Plans provide bonus to Infantry or Cavalry units (eg: Flank or Infantry). Rules define three unit types: Ground Troops; Cavalry; Siege Engines and Walls.
a) Does Cavalry in Battle Plans apply to all cavalry units or just LC and HC?
b) Does Infantry in Battle Plans apply specifically only to infantry units or to all Ground Troops?
If you look on page 7, you'll see that Infantry is one of the types of ground troops; the ones marked IN. You'll also see that Cavalry is a header covering three types: Chariots, Heavy Cavalry and Light Cavalry. That is how I play it.
2) The Rules define the concept of Force Advantage (# of Macedonian minus # of Enemy units). The Intimidation die roll modifier refers to Force Difference. Is it the same concept?
They are calculated the same way, but used differently. Force Advantage works with Battle plans, but you must have more than your opponent in order to use it. Force Difference is used when attacking Strongholds, and applies whether positive or negative (see the Stronghold section of the Player Log).