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Given the "Line Endings" options set to "Force Newline", working on java file. I tried this in two cases (1) File initially had NL endings (2) File initially had CRLF endings In both cases when licensechanger completed, the newly inserted license header had CRLF endings. The rest of the file had NL endings. Interestingly, case (2) shows that the option mostly works and only fails for stuff from license.txt. BTW, the license.txt file on disk had NL endings.
Thanks for spotting this bug. The issue should be resolved within the next version.
Fixed in changeset http://hg.netbeans.org/main/contrib/rev/129e2a086639.