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Backwards compatibility:
You cannot remove the sr?_replace options. calibre saves previously used conversion settings. Your change would render the saved settings useless. Instead leave them be and add another option. Have the GUI use the new option for new conversions, pre-populating it with the values from the sr? options, if they exist. In the case where values exist for both, ignore the old ones.
Internationalization
You only need to mark strings with _() in .py files. .ui files are handled automatically. That's all you need to do.
UI
Why not use both the explicitly added expressions and the values in the textboxes, if they exist.
CLI
How are you serializing multiple expressions on a single command line option?
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