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The problem is that the Calibre internal directory structure cannot be changed without a major rewrite. Assumptions about the current structure permeate much of the code.
That means that if you cannot live with the Calibre internal structure then you will not be able to use Calibre for library management.
You can still use the Calibre conversion facilities if you use the command line utilities as there you provide the paths for both the input and output files.
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