What’s the best way to organize scattered Windows config files with Chezmoi?

You generally don’t need to move or link anything. Chezmoi can manage files wherever applications expect them, so you can add each config from its normal location and let Chezmoi track it there. I’d avoid symlinks and junctions unless a specific application requires them. PowerShell profiles and files affected by OneDrive may need a small Windows-specific script to copy or place them correctly.

A practical setup is to use Chezmoi’s templates and source paths for the different locations, while keeping PowerShell-specific setup in your profile. Scoop and Chezmoi work well together as command-line tools used from PowerShell; Scoop installs the programs, and Chezmoi manages their configuration. Test each application individually rather than creating links for everything at once.

Using XDG_CONFIG_HOME is perfectly reasonable for programs that support it, and keeping those files under .config can make the layout cleaner. For applications that ignore XDG_CONFIG_HOME, though, it’s usually simpler to leave the files in %APPDATA%, a Scoop persist directory, or wherever the program expects them. Chezmoi doesn’t require every configuration file to share one directory.