New versions of MySQL WorkBench have an option to change specific timeouts.
For me it was under Edit → Preferences → SQL Editor → DBMS connection read time out (in seconds): 600
Changed the value to 6000.
Also unchecked limit rows as putting a limit in every time I want to search the whole data set gets tiresome.
与恶龙缠斗过久,自身亦成为恶龙;凝视深渊过久,深渊将回以凝视…