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You can open the html in the input directory and leave all the   there, but then you're on you're own to fix all the other problems in the document - once you've done that you can import it back to Calibre as html.
The problem is that the poppler libraries stick   everywhere, and in order to do all the things to fix a typical novel they get removed first. There are probably other approaches that can be taken in the code, but investing significant effort in the existing pdf conversion engine isn't worth it since it's going to go away.
Blocks of code examples are always going to be a sticky problem regardless of what happens in the future.
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