I guess I find it useful to look at my packages and files and know by their names to what activity/fragment/adapter etc they correspond to, however, I understand your point that in a really big project one might end with a LOT of files. It really depends on the size and scope of the project. I guess you could choose whichever you and your team feel comfortable with as long as it fits with your team's standards since the ultimate goal of setting a structure is to make it readable and maintainable to those who will work on it.
I know it's a very general answer, but still, hope it helps. And thanks for reading the post, hope it helped as well.
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