I have been told that Wishes work differently in Commander than in normal casual Free-For-All (FFA) mtg. Do the comprehensive rules cover how wishes work in Commander? Do the rules for wishes differ from normal FFA multiplayer?
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Wishes are non-functional in Commander, unless your group specifically allows sideboards.
Basically the Rules Committee's reasoning was that using wishes in their original, casual-play way (searching your entire collection) wastes too much time in play1. So they restrict you to searching your sideboard, which is how wishes work in competitive MTG. However, Commander's sideboards are "optional" and Sheldon has generally come out against them, so the default is that wish cards don't work at all.
Sideboards still have to follow all the normal deck-construction limitations, like in any other format; for Commander, this means you can't have break the one-of restriction or violate color identity just because a card is in the sideboard. Thus, if you group agrees to play with wishboards, you'll still be limited to your commander's color identity.
(Note also that the official sideboard size is 10 cards, not 15 like 60-card constructed.)
1 – Which is also why Shahrazad was finally banned after some time as the only Vintage-banned card legal in Commander.
I have done a search for all Commander references in the CompRules and have found nothing specific. There are several points to consider when determining this question in particular: