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When in compare editor, manually copying changes from right to left causes the copied hunk to appear as conflict in the Sync View. This is similar to bug 300213.
We can either disable this kind of interaction with changes and limit it to "Merge" action only. Or figure out which hunk is associated with the change being copied and mark it as merged (applied). The only problem is that a hunk can contain many changes and cannot be considered as applied until all of them are copied, so this may be a little bit tricky.
Created attachment 160329 [details] Fix v01 Restored "Mark as Merged" action. It should be used to manually mark a file as merged after copying changes via the toolbar action in compare editor. This is an early version of the fix, do not apply.
Created attachment 160330 [details] mylyn/context/zip
Created attachment 160489 [details] Fix v02 A polished version of Fix v01. One more thing needs fixing though, you cannot select an individual hunk and mark it as merged. This is a similar issue as bug 300214 and should be addressed there eventually.
Applied to HEAD, available in builds >N20100228-2000. "Mark as Merged" is back!