The current information is in the first post of this thread. There are links to the plugins as well. We cannot give detailed instructions about installing and using them, though - DRM removal is illegal in some jurisdictions, even for personal use.
As to importing your files to Calibre, just use the Add Books button in Calibre. If you right-click on it, there are several options to import from folders.
Note that you cannot retain your folder and subfolder system in a calibre library - that is not possible. In Calibre, you use metadata, tags, custom columns, virtual libraries and the like to sort and categorize your books, not folders.
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