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Modifying source code and having your changes preserved through updates is easy. Just use bzr merge to update the source and it will preserve your changes, unless there is a conflicting change (which is unlikely since this part of the calibre code is pretty stable).
There is no shortcut to magically explode to html and repack to arbitrary format. You have to run a full conversion pipeline for that. You can do it for particular formats, see the tweak book function in calibre or the modify epub plugin, but in the general case a full pipeline run is required, as some output plugins depend on the normalization that occurs during a pipeline run.
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