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I have configured the code formatter in the "New Lines" tab and checked the "at end of file" checkbox. When a Java class ends with a comment, e.g. public class MyClass { } // comment with no "new line" at the end the code formatter doesn't add a new line. But the new line is correctly added when the last comment isn't there, or the comment is a /* ... */ comment.
Released for 3.3M5. Added regression tests org.eclipse.jdt.core.tests.formatter.FormatterRegressionTests#test643-649
Verified for 3.3 M5 using build I20070205-0009