[tikhonj]

They work well with per-directory settings. It's a simple convention and it works really well for things like .git, .gitignore, language-specific settings files and so on.

Putting files and directories like this inside another directory would not win you much, especially if you only have one in a given location (e.g. you only have a .git directory). But you wouldn't want to keep tripping over your .git directories either!

However, having a dedicated directory for configuration files applying to a user or the whole system is a different story. I would much rather just have a ~/config directory than a home folder full of dot files.