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It appears that the default behaviour is to strip PHP from editor content. In my local out-of-the-box copy of v2.3.2, if I select 'source' mode in the editor and type in something like:
<?php function(); ?>
RE: Preserving PHP content in the editor?
FCKConfig.ProtectedSource.Add( /<\?[\s\S]*?\?>/g ) ;
RE: Preserving PHP content in the editor?
$oFCKeditor->Config['ProtectedSource'] .= '/<\?[\s\S]*?\?>/g';