Look into using SourceDir, eg.

<File .. Source='SourceDir\include\foo.h'/>

You can use the -b linker option to specify the exact location of SourceDir. 
See also -

http://stackoverflow.com/questions/1811035/spaces-in-my-wix-source-path


Martin Sustrik-2 wrote
> 
> Hi,
> 
> My source tree has a file in "include" subdirectory. I want to install
> it to "include" subdirectory on the target box.
> 
> I do the following:
> 
>          <Directory
>              Id='TARGETDIR'
>              Name='SourceDir'>
> 
>              <Directory
>                  Id='ProgramFilesFolder'
>                  Name='PFiles'>
> 
>                  <Directory
>                      Id='INSTALLDIR'
>                      Name='Foo'>
> 
>                      <Directory
>                          Id='include'
>                          Name='include'>
> 
>                          <Component
>                              Id='core_include'
>                              Guid='...'>
> 
>                              <File
>                                  Id='foo.h'
>                                  Name='foo.h'
>                                  DiskId='1'
>                                  Source='foo.h'/>
> 
> Light.exe is looking for the foo.h in the main directory (where
> light.exe is run from) rather than in "include" subdirectory:
> 
> C:\Users\me\libxs\foo.wxs(98) : error LGHT0103 : The system cannot find
> the file 'foo.h'.
> 
> Any ideas?
> Martin
> 
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