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If line endings are in Windows format (CRLF), the commit viewer shows additional empty lines in the diff tab. Tested on Windows and Linux.
Can you post a screenshot of this or a link to a commit that shows the behavior?
Example commit is 862a05dd760c9dc27d1231824ea00a8b5085caac from git://git.eclipse.org/gitroot/mylyn/org.eclipse.mylyn.reviews.git
Great thanks, that made it very easy to debug, proposed fix pushed to: http://egit.eclipse.org/r/#change,4273
merged as 741a4fd2fc001e639a16b7e68773eb4154e34cc8