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calibre's source control system has moved from bzr to git, see the sticky post in the development section. Other than that, the code layout is mostly the same. You have two ways you can approach this:
1) Make copy to library use merging code optionally. As I recall, it already does this in some circumstances, search for auto_merged_ids in actions/copy_to_library.py for details. You might need to improve it a bit to do exactly what you need.
2) Create a simple plugin that automates merging duplicates found by Find Duplicates, or extend Find Duplicates to do that.
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