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To reproduce: open a Java source file with UNIX line endings, make a simple change, and save the file. Now the source file has Windows line endings. I've tried with a couple of other file types (e.g. .html and .sql), and those work as expected and don't change the line endings upon saving. Product Version: NetBeans IDE Dev (Build 201602090002) Updates: Updates available Java: 1.8.0_74; Java HotSpot(TM) 64-Bit Server VM 25.74-b02 Runtime: Java(TM) SE Runtime Environment 1.8.0_74-b02 System: Windows 7 version 6.1 running on amd64; Cp1252; en_US (nb)