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Originally Posted by tomsem
Kovid answered some of my questions about this and didn't seem to think anything calibre is doing would interfere. But hopefully he or some of the other developers will be poking around to make sure.
If you don't like what calibre (or want to see what it does), turn on debug mode and look at the intermediate HTML files that will be left around. Then you can edit and build mobi from those.
In any case, no automatic conversion should be considered 'commercial grade', though evidently a lot of big publishers just have their epub files run through kindlegen. The most obvious artifact of this is where chapter navigation only hits the top level, e.g. 'Part 1, Part 2, etc.' rather than all the chapters in between.
You might also want to look for a python script named 'kindlestrip'. It will significantly reduce the file sizes of mobi generated by kindlegen/kindle previewer, by removing the source files archived in the file. Or just send them to Amazon to put in your PD library, they strip the source archive (if there's one in there) before storing it.
Someday I hope amazon will add .epub to the formats that the conversion service handles.
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Thanks for your answer!
About the problem, maybe it is gone, maybe it isn't (and the threads about it maybe long buried), I have my routine now and am sure that kindlegen always does what I want (and that doesn't mean I don't like calibre, it's awesome). I'm not using python so I'm not using kindlestrip but it's ok, the file size really isn't that important to me. And maybe "Personal Documents" helps now anyway keep the file sizes small. And yeah I hope too that someday we'll be able to convert epub to Kindle without much of a hassle via email...