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How to restore data after MySQL Upgrade?

I upgraded from MySQL 5.5 to 5.6 by uninstalling 5.5 and then installing MySQL 5.6. Now that MySQL 5.6 is running, none of my DBs or data is present/visible in MySQL Workbench. I also see that I ...
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Unknown option '--no-beep'

I installed a new version of MySQL server (previously 5.0, now 5.5) and I copied the data folder in to the new one. Now I should perform mysql_upgrade. I opened the command prompt (server is located ...
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