In winning three World Series, the Giants used their farm system effectively to stock their big-league club and trade for help. Things have changed. The system is not barren, but the flow of prospects to the big club has slowed, and the Giants acknowledge that a dearth of sexy top-100 prospects hinders them in trade talks. “It’s fair to say our system is not as strong as we’d like it to be, and it does sometimes cost us deals,” general manager Bobby Evans said Wednesday. “That’s reality.” The Giants hope to change the reality. They expect to replenish their prospect stock through their No. 2 slot in June’s amateur draft and more international spending. Beyond that, Evans revealed he has spearheaded what he called a “significant rebuild” of the farm system. That includes big changes in personnel under new farm director David Bell that could be announced Thursday. The Giants are creating positions for assistant directors of player personnel, adding a fourth coach to each farm club, putting sports-science specialist Geoff Head in charge of the minor-league medical and training staff, with other changes designed to better prepare players to win big-league jobs.