The trick JDT made was switching to the new API in Compare added in 3.5. The crucial part is org.eclipse.compare.contentmergeviewer.TextMergeViewer.getEd itorInput(ISourceViewer), which allows JavaMergeViewer to create a CompilationUnitEditorAdapter object (a subclass of JavaEditor, a real editor, not a viewer).
For TextMergeViewer see this bug. Don't know if guys from CDT have something similar on their list.
Is there anywhere we could voice our support for fixing this bug sooner rather than later?(or at least the Displaying-Markers for TextMergeViewer part?)
Just to describe our need: we have a code review tool with 500 active users and growing. Most of the users like to do their code reviews in CompareEditor(in order to review only the changed code), but currently only the Java developers can actually see their comments(as markers) in the Compare Editor. It's a useful tool and it also introduces a lot of developers to Eclipse for the first time.