If you open the Miscellaneous page of the preferences, there is a button to open the configuration directory. A lot of the configuration is stored in there. Backing up this directory will allow you to restore a large percentage of the configuration. This includes the icons in the menus and the preferences.
But, some configuration is store at the library level. In this case, the configuration is usually stored in the libraries database. Most plugins do this if they support different configurations per library.
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