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There isn't any design documentation, beyond a brief outline of the code structure in the development section of the User Manual, but feel free to ask any questions and I'll try my best to answer.
On a tangential note, I developed calibre without the use of a debugger and still don't use one today. But python comes witha nice debugging module called pdb. You can use it to do interactive debugging via the command line. Just run
calibre-debug
and you will get a python prompt with a fully initialized calibre environment. You can them import the pdb module and do whatever debugging you want.
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