Sometimes you have to do work with Unix/Linux machines and the differences in new line encodings can be annoying, especially when doing diffs or merges.
Luckily, Eclipse has options for this which covers a global and per-project scope.
To change the option globally:
1. Open the preferences dialog.
2. Select "General" > "Workspace".
3. Change the "New text file line delimiter" to "Other" and select your preference.
To change the option on a per-project basis:
1. Open the project.
2. View the project properties.
3. Select "Resource"
4. Change it from "Inherited from container" to "Other" and select your preference.
If your project is using UTF8, you might want to take the time to change it to UTF8 while you're at it.