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Problem annotations and markers (in the Problems View) should work for files that are not in the workspace. A related enhancement (74113) has already been fixed for displaying error annotations in an external Ant build file. Right now, the only workaround is to create a linked resource for the external file. But that's all it is, a "workaround." There should be a nicer way of doing this since not every eclipse application will revolve around a workspace.
*** This bug has been marked as a duplicate of 22284 ***