Question! Was searching comments before asking this same question. I found the file that you mentioned, but I only see the scythe and bug net here. Is there not one for axe and hoe? The reference sheet doesnt mention which one to use, and the only sprites I see for these are not aligned. So wasn't sure if there was one like the scythe and bugnet that is already aligned for use.
The axe, pick, and hoe work in the same way as weapons. They come in a variety of different angles. You will need to choose the sprites you like and position them in a way that works for you. Once you configure one, you'll be able to swap out the sprite sheet for the tool and the animation will still work with any other tool you put in its place, since they're all laid out the same way.