> 1. For config, it spreads the config across a bunch of nested directories, making it hard to read and write it without some sort of special tool that shows it all to you at once. Sure, you can easily edit 50 files from all sorts of directories in your text editor, but that’s pretty painful.

It really depends how comfortable you are using the shell and which one you use.

cat, tree, sed, grep, etc will get you quite far and one might argue that it is simpler to master than vim and various format. Actually mastering VSCode also takes a lot of efforts.

> 2. For data storage is that lots of smaller files will waste partial storage blocks in many file systems. Some do coalesce small files, but many don’t.

> 3. For both, it’s often going to be higher performance to read a single file from start to finish than a bunch of files. Most file systems will try to keep file blocks in mostly sequential order (defrag’d), whereas they don’t typically do that for multiple files in different directories. SSD makes this mostly a non-issue these days, however. You still have the issue of openings, closings, and more read calls, however.

Agreed but for most use case here it really doesn't matter and if I need to optimise storage I will need a database anyway.

And I sincerely believe that most micro optimisations at the filesystem level are cancelled by running most editors with data format support enabled....