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The project format changed. Now, files in the directory are automatically included in the project. This makes Modlr unable to find them in the project file, and Codegen has become sketchy.

Add this to Project:

  <EnableDefaultCompileItems>false</EnableDefaultCompileItems>
</PropertyGroup>

Also, make sure you have this dependency on files:

<Compile Update="EcoProject1\Class3.eco.cs">
  <DependentUpon>Class3.cs</DependentUpon>
</Compile>

This should be fixed in FW.

See also: Codegen failed, Code generation not working