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BR
Portable requires the first (default-starting) Library to be where it is, You can have additional libraries with portable.
Nothingness
Calibre will recreate the configuration folder if missing from the expected location.
There are 23 folders in my Local Settings\application data
There are 39 folders in my Application Data
Ubuntu puts things in the dot config folder
Unless you have taken steps to set your OS to use alternate locations for system type folders
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