I love this tweet: "Long names, flat folders"
Multiple files with same name is unclear - typing index.js in a project with hundreds of them is not a good time. Needless categorisation and sorting is not very useful, and having a bunch of folders with only one or two files is just frustrating to navigate.
Browsing relevant files for an app is way easier if I can just see a list without clicking through folders all the time. Grouping can be done with filename prefixes/suffixes.
Fewer folders, longer filenames!