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Make command-line options order-independent (DM-21890)
This commit appears on DM-21889 branch even though the ticket for it is DM-21890, this is to minimize the number of incompatible merges. All global/top-level options have been removed and copied to each sub-command (where they make sense). I have also refactored the code that makes options into a number of separate methods, this makes it cleaner and should also prepare us for the next step of refactoring. All unit tests were updated for new command line interface.
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