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The user.js file, located in the profile folder, is used to customize preference settings in Mozilla-based programs. When you launch the application, the valid preferences you've added to user.js are then automatically copied into the prefs.js file (also located in the same profile folder), which stores all the preferences for the current user. For that reason, before you create or edit the user.js file it is advisable to make a backup copy of the prefs.js file. Although the prefs.js file can be modified using (about:config) or through the options and preference settings within the Firefox/Thunderbird/Mozilla Suite program's user-interface, the preferences you add via the user.js file will never be modified unless you yourself edit the user.js file contents.
The last part is the nice thing about using user.js instead of about:config