Reports

To get to the settings (just hit Ctrl + Alt + S), go to Editor > Code Style > General. Next, choose the option you want for the line separator.
In Project View, click on the directory (probably your whole project) to select it. Then, go to File > File Properties > Line Separators and choose the line separator you picked in Settings. Be aware that if you have a lot of files, your IDE might take a minute or two to process. No big deal, just wait.
After that, go to the commit view (Alt + 0). Select all files and do a rollback. This will roll back all changes but keep the line separator settings.

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