You need to understand me here, i registered on this forum just for this.
In today's world, consumer is the king. I have a 10gb collection of ebooks which keeps ever increasing so i dont want calibre to use another 10gb just in case i want to move to another software and want my original directory structure intact. Its illogical and inconvenient.
I am too a coder and probably think that the developer will have to do a rewrite of a major portion of code and algo's to do what i have asked. But let me tell you, sooner or later more ebook managers will come in the software world and then people will choose them over calibre just because of this.
I use as an alternative Alfa ebooks manager. I had to pay for it though but i had no choice.