What does the title The Chocolate War mean?

The fight that that Jerry Renault has with the underground gang The Vigils is over the annual chocolate sale run by Trinity High School.  The evil temporary headmaster, Brother Leon, has made an exorbitantly high quota for each boy to sell (50 boxes).  The only way Brother Leon's avarice can be satisfied is by cooperation with The Vigils -- which means turning a blind eye to their bullying and coercive practices.  When Jerry refuses to sell chocolates he incites the wrath of both the school administration headed up by Brother Leon, and, most especially, The Vigils headed by Archie Costello, with his loathsome enforcer Emile. 

It becomes a "War" when Jerry stands fast in his refusal to sell he chocolates, no matter how many veiled threats Brother Leon makes, or how many physical and psychological attacks he endures from The Vigils.  Goober, Jerry's best friend, originally started out on Jerry's side, refusing to sell the chocolates, but in the end Goober cannot take the pressure and gives in.  This doesn't make Jerry's defiance easier, but it does give him the kind of resolve which makes him even more determined not to back down.  At one point, it becomes clear to Jerry that if he gave into The Vigils that he'd be losing a major part of his own self-esteem.  It was easier for him to suffer the abuse of his fellows, and his complete ostracising from their society, than it was for him to give in to their unreasonable demands.

Finally, when Jerry is nearly beaten to death, he gives in to the beating because he cannot stand alone against so many ranged against him.  But he holds out long enough that one of the teachers finds out about the staged fight; and Jerry is saved from being actually killed by Emile in an unfair fight.  At this, the end of the book, the word "war" become even more poignant.  Jerry stood his ground as long as he could, and stood up for what he thought was right.  In the end, however, he couldn't stand by himself against an angry mob -- the whole idea of the war between The Vigils and Jerry brought out the worst in the boys of Trinity, and very nearly killed Jerry.  But through the conflict Jerry learned something about himself.  He learned that standing up to tyranny doesn't always work (he had to be saved by an outside agency) but it is the only thing that can be done in the face of an unjust majority.