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The only files that would be modified by the Make VS.NET action are the RC file (C++ projects only) and/or AssemblyInfo file (if any versions or properties are being set/incremented) and the project file (if the base address is being modified), and it will log these changes if they are made.
The read-only attribute of any files opened for editing normally gets set by Perforce during a submit/revert unchanged. You can take a look at the Perforce.bld sample or the VisBuildPro.bld sample in Samples\VisBuildPro to see how we do edit/commit during the build.
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