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I am sure others will have things to say about this, but here are a few points.
Calibre managing its own e-book files is a fundamental design decision that isn't going to change. There is no way that a plugin can affect this. If you insist on having the book files be under your control then calibre isn't going to work well for you.
One way to work around it is to have the files that you import just be pointers to the actual files, something like m3u playlists for music files. But by doing this you will lose most of the capabilities of calibre. It needs the actual book content for most functions.
If calibre takes 20 minutes to import 100 books then something is wrong. It works far faster for me.
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