wp_options table has duplicate rows and primary key / autoincrement has been removed

Well after a lot of digging, I think I uncovered what happened. The clue came from the fact that I noticed it was wp_options and all alphabetically subsequent tables that lost their primary keys.

On import, first the tables are created. Next it goes through all those tables in alphabetical order and applies the primary keys and auto_increment flags. It would seem the application of keys and flags was interrupted just prior to wp_options and the failure cascaded down.

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