I know how to set the permissions for a folder:
<DirectoryRef Id="ProgramFilesFolder">
<Directory Id="PHPFolder" Name="PHP">
<Component Id="PHP_comp" DiskId="1" Guid="*">
<CreateFolder>
<Permission User="Everyone" GenericAll="yes" />
</CreateFolder>
However I need the permissions to be applied to all subfolders as well. Is this possible with out listing all the folders?
First of all, I would recommend you using PermissionEx instead. It is a standard WiX extension and it has one really huge advantage over Permission - it doesn't overwrite, but modifies ACLs. And by default, it applies permissions to the folder and all its descendant files and folders, so you don't have to specify anything extra.
Hope this helps.