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At some point I installed MySQL Workbench 5.2.47 Revision 10398. This version has the feature to reformat an SQL query located at:
Plugins > Utilities > Reformat SQL Query
I like this feature and I use it almost every day.
Now every newer version I downloaded from http://dev.mysql.com/downloads/workbench/ misses this feature.
How do I get it back?
Just answering my own question. I found the feature by accident. It was moved and renamed to and is now located here:
Edit > Format > Beautify Query
Shortcut: Ctrl+B