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I20111018-0850 The API Tools quick fix to remove an unused API problem filter changes all line delimiters in .api_filters to the platform default delimiter (Windows, in my case). Operations on existing files must always use the existing delimiter format. For new files, the Platform.PREF_LINE_SEPARATOR preference must be used (but the quick fix doesn't even respect that option, which is set to \n in my case).
Fixed in master: http://git.eclipse.org/c/pde/eclipse.pde.ui.git/commit/?id=ab64fff09e017c0471e09730735ee099fedad75e