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VEX currently discards any comments in the XML document. It needs to preserve these comments so that they are rewritten back to the XML file when saving.
Moved to Mylyn Docs Vex.
With http://git.eclipse.org/c/mylyn/org.eclipse.mylyn.docs.vex.git/commit/?id=8dec4d884b9a9276133b8eb92eb28ce6dd5328e5 Vex can handle comments within the root element now. If you have comments before or after the root element, those are still discarded. Support for "outer comments" requires a major refactoring of the DOM since Document can have only one child (namely its RootElement) at the moment. I would suggest to postpone this major refactoring until we have released 1.0.
I added the markers <!-- and --> as static text before resp. after comments.
The "big scary refactoring" has taken place and I was finally able to add also support for comments outside the root element. (f57b809)
Released 1.1.0 M1