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For those who already have calibre installed and want to try a version that utilizes the method(s) Kovid mentioned, the attached script has the advantage(?) of updating the existing epub, instead of creating a new epub that contains the changes.
** WARNING!! Make sure you have good backups of any epubs you try it with, because it WILL modify the epub you feed it!! **
As Kovid mentioned earlier, run the script like this:
calibre-debug cm2em_calibre.py file.epub
(assuming, of course, that 'cm2em_calibre.py' and 'file.epub' are in the current directory)
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