Replaces the original version.
Nintendo replaced today, Animal Crossing: New Leaf on the Nintendo 3DS eShop with Animal Crossing: New Leaf – Welcome amiibo.
The convenient download includes the "Welcome amiibo" update in one download. Buyers previously needed to download two files before they could take advantage of that free update.
New features in "Welcome amiibo" includes: support for all Animal crossing amiibo figures and cards; new villagers; a new Campground; and more.
If for whatever reason you want to play the first version of that title, you can always purchase the physical version that doesn't include the "Welcome amiibo" update.
Image credit: Nintendo