Use the Windows Terminal app with PowerShell when running auto-editor commands. Using the CMD shell isn't impossible, but you'll have to escape commands differently than shown in the docs.
A terminal is a GUI program that manages shells. It handles features like scrolling through history, and copy paste. A shell is a program that interacts with OS. Having a modern terminal means the terminal will look beautiful instead of ugly. Having a modern shell installed makes scripting much easier.
CMD is the older terminal/shell that Windows keeps around for compatibily reasons. I recommend using Windows Terminal plus Powershell instead.
Auto-Editor doesn't have an option that batch processes files, but you can achieve the same effect with a simple PowerShell script.
# Save to a new file with a ".ps1" extension
$files = "C:\Users\WyattBlue\MyDir\"
foreach ($f in Get-ChildItem $files) {
auto-editor $(Join-Path -Path $files -ChildPath $f)
}