E-commerce startup Shopify only got into brick-and-mortar commerce last August, but it’s already retooling its transaction structure with the aim of making it a more competitive option to rising in-store payments giant Square. It recently updated the per-swipe rates it’s charging on credit card transactions for its Apple iPad-based point-of-sale system. Shopify actually raised the percentage it takes off each transaction, but it has eliminated the per-swipe fee on every card purchase. For instance, its basic rate transaction charge has increased from 2.5 percent of purchases to 2.7 percent, but it no longer charges the 30-cent fee on every transaction. That winds up being a big benefit to merchants who do a lot of transactions for low dollar amounts, though merchants who deal in larger amounts end up paying more under the new rates (for the basic plan the crossover point is $150).