I would not draw that conclusion, but I don't have enough information.

My guess is that you have a MSBuild script which is building some
application project (maybe in VS or not) and that there is an 'output'
folder full of generated files.

Then my guess is that, as part of building the wix project, the MSBuild
script either launches a cmd file that launches <path to wix
tools>\heat.exe, or more likely the MSBuild script either uses a
HarvestDirectory, HarvestProject or a Heat task (all documented in the wix
chm) which results in generated wxs files.  There may likely be an XSLT
file, also used in one of the above commands to call heat which causes
certain harvested files to be excluded from the wxs results. (This is often
desirable depending on how you want to design your project.)

I guess that there is some custom MSBuild script that makes its own list of
the files in the 'output' folder and then parses the generated WXS file to
stop the build process if it thinks that something was not authored
correctly.

But all of the above are as I said guesses, and what you want to do to
change the results depends on the unknown details. 



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