chezmoi doctor marks .config/chezmoi/chezmoi.toml as suspicious.

[jmigual]

In my dotfiles repo (https://github.com/jmigual/dotfiles) I have a very basic chezmoi.toml:

[diff]
    exclude = ["scripts"]

And it is marked as suspicious. I don't know why.

[twpayne]

This is correct. You should use a config file template instead.