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Thanks @robmen! I actually found your tutorial series on YouTube and it helped me figure out the gap in my knowledge: Directory and File tags refer to "where files end up" and the attributes refer to "where they come from." I was also couldn't find the variable that this tool used for source files (ie before packaging) that can go within a Source attribute's value. Here is the code that ended up working for me:

    <DirectoryRef Id="INSTALLDIR">
      <Directory Id="INSTALLDIRBIN" Name="bin" >
        <Component Id="MsixComponent">
          <File Id="JavaExeFile" Source="$(var.ReproDir)\bin\java.exe" >
            <msix:Application Id="OpenJDKApplication" />
          </File>
        </C…

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@robmen
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@jmjaffe37
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