The comparison editor is really different from the standard editors, each functionality must be redefined for it. You should encode it yourself (as far as I know), but you can look at the implementation of the original editor for tips.
In the case of Eclipse, AbstractDecoratedTextEditor implements marker display functionality (that is, a descendant of the TextEditor class). What makes this functionality difficult to implement in the case of Compare editors is that the comparison editor opens two resources at once, so it’s more difficult to put each marker in the right place (I think why it is not implemented as a whole).
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