You have to remove the ylim function and input the scale_y_continuous one
ggplot(data=test, aes(x=Var2, y=value, fill=Var1))+
geom_bar(stat="identity", position=position_dodge(), colour="black")+
scale_fill_manual(values=c("grey80","grey20","blue","lightblue"))+
theme_bw()+
scale_y_continuous(breaks = seq(0, 1, .1), limits = c(0, 1)) +
ggtitle("example")+
#theme(legend.direction="horizontal",
# legend.key.size=unit(18,"points"),
# legend.justification=c(1,1),
# legend.position=c(1,0.25),
# legend.title=element_blank()) +
scale_x_continuous(limits = c(-7.5,7.5), breaks = round(seq(-7,7)),1)+
xlab("position")+ylab("arbitrary value")+
geom_hline(yintercept = 0.5, linetype=3)