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The 48-year-old has previously served the Cappielow club as a player, development squad coach, interim manager and assistant.
Hopkin is a former Scotland internationalist who guided Livingston from Ladbrokes League 1 to the Premiership before a spell as Bradford City boss.
Chairman Crawford Rae told the club website: "David is a phenomenal coach and we are delighted that he will be working to further develop our home-grown talent while building a squad that will hopefully bring absent supporters back to Cappielow."
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