When using the code cleaner, it feels it simply MUST add extra tags I don't need!

For example, I use a lot of includes - so there's one for my page headers and nav. The cleaner insists on adding closing </body> and </html> tags, regardless of what I've got unchecked in the prefs.

Any way to get it to NOT do that? Just pretty the code, but don't add anything?

There aren't any settings in the code cleaner particularly for PHP documents. I also use includes, but I never run the include files through the code cleaner.