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> The first benefit is that it removes clutters from your $HOME.

Invisible clutter? That's a strange concept.

But the rest of your point indeed makes sense. It still is easier and probably comment to backup the whole $HOME. But those points you can see as a benefit, though not obvious.

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As Rob mentions in his post, the more dotfiles there are in $HOME the slower path resolution for any subfiles becomes. How do we navigate to ./src? We open the directory and read all the entries until we find the one called "src". What happens if we encounter a morass of dotfiles beforehand? src takes a while to find. The clutter may be invisible to you, but it does gum up the works.

Unless you have many thousands of files, I can't imagine you would ever notice a slowdown.

For what it's worth, most modern file systems (JFS, XFS, ext4, reiserfs, btrfs, ...) have logarithmic (or better) directory lookup times. This is achieved using hashes and b-trees (or even hash tables).

Fair point. Though anything using the standard POSIX dirent API would still get the performance hit (even if path resolution doesn't).

It's not invisible when you're actually looking for an invisible file.

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