A quick scan of the code shows that it runs mix format inside the first directory where it find a .formatter.exs file for the file being checked.
If I cd into the migrations directory and run mix format etc then I get the exact same error that the package reports.
The workaround is to delete .formatter.exs from the migrations directory. It’s already checked in the configuration inside .formatter.exs in the root directory. Then it works
So the lesson is atom-elixir-formatter can only be run on sub-directories that don’t have a .formatter.exs
