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From WiX Wiki at MindCapers

Problem description

Attempting to compile and link a Wix project produces the following error.

:'''ICE64''': The directory ''<dirname>'' is in the user profile but is not listed in the RemoveFile table.

Explanation

Folders that contain files are implicitly added to the remove table. Folders that contain only shortcuts or registry values, and which do not contain files, must be explicitly added to the remove table. This has not been done.

Solution

Explicitly add the folder to the remove table by placing the following code in your directory creation section. The <RemoveFolder> element fixes ICE64. You may have your shortcut definition within this component or place, such as a fragment. You also need to add a <ComponentRef> element to your Feature section.

  <Directory Id='ProgramMenuFolder' Name='ProgramMenuFolder'>
     <Directory Id='IDProgramGroup' Name='Company'>  
        <Component Id='IDProgramGroup' Guid='insert valid Guid here'>
           <RemoveFolder Id='IDProgramGroup' On='uninstall'/>
           <RegistryValue Root='HKCU' Key='SOFTWARE\Company\MyApp'
                          Type='string' Value='Hello World' 
                          KeyPath='yes' />                                    
        </Component>
     </Directory>
  </Directory>