You should not always use each and every sql commands that this tool generates. For example doctrine does not recognize "unsigned" ineteger but MySQL gives error if you want to add constraint key to that coloumn that is not set as unsigned so you should set it "unsigned" manually so when you run the tool it gives a sql command to remove "unsigned" and set it as a simple integer. So sometimes you should output the sql commands generated by the tool into a file by appending >file.txt at the end of console command then edit the sql commands in file as desired then run them via database console.
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