Add a *.csproj to the root of your project (or an ancestor directory). It will be the target, can be named anything, and contains the following:

Code2Format.csproj

<Project xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
  <ItemGroup>
    <Compile Include=".cs" />
    <Compile Include=".**.cs" />
  </ItemGroup>
  <Target Name="Compile">
    <Csc Sources="@(Compile)"/>
  </Target>
</Project>

Then run the following command:

.\CodeFormatter.exe path\to\Code2Format.csproj /nocopyright /aggressive

This assumes that you've already cloned and built the codeformatter repo.