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The Make VS.NET action will currently match and update versions/properties in any source files named like *AssemblyInfo.*. This should probably be restricted to match on AssemblyInfo.* instead. For now, a few workarounds:
1) Create a separate Make VS.NET step (with Don't build checked) to set properties on the CommonAssemblyInfo file (and don't set those properties from the step that builds the solutions).
2) Set your build step(s) to not set those properties, then use a Process Files steps to iterate over all AssemblyInfo.* files, and a child Make VS.NET step (with Don't build checked) to set versions/properties as desired.
3) Rename your common files to not end in AssemblyInfo.vb (i.e., AssemblyInfoCommon.vb, CommonInfo.vb, CommonProperties.vb, etc.)
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