I think I have found an issue with WIX.
In my solution I try to keep project names short and only put the full namespace on the output files. So something like
Organisation.Application.Data
Oragnisation.Application.Data.DAL.Entity
would appear in my solution simply as
Data
Data.DAL.Entity
but the project properties would have the full namespaces on the output file etc
Now in VS when you click "Add Reference" and add a project reference, these will show up as
Data (Data\Data)
Data.DAL.Entity
Don't ask me why the one without a "." gets a bracketed qualification cos I have no idea.
Adding a reference to a WIX project does the same.
Now in my WXS file I have something like this
<file id="user-content-Data" name="$(var.Data.TargetFileName)" keypath="no" assembly="no" vital="yes" checksum="yes" source="$(var.Data.TargetPath)" --="">
<file id="user-content-Data.DAL.Entity" name="$(var.Data.DAL.Entity.TargetFileName)" keypath="no" assembly="no" vital="yes" checksum="yes" source="$(var.Data.DAL.Entity.TargetPath)"></file></file>
The $(var.Data.targetFileName) causes a compilation errors whereas $(var.Data.DAL.Entity.TargetFileName) works fine.
It seems these () qualified references break the "var" system in some way.
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