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we must have a correct indentation when writing the SBML file, even if it is not suppose to be seen by human :-)
As far as I see, there are only two problems left:
1. Indentiation for arbitrary annotations
2. One-line tags for elemens such as <species... />, <compartment.../> don't work at the moment, it always creates a separate closing tag.
I forgot one; how about notes? The indentation might also cause problems there.
as a temporary solution (or not ?), we could try to use http://htmlcleaner.sourceforge.net/index.php