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I have two installations of MySQL on my machine, with the following paths to executables: /usr/local/mysql/bin/mysql /Applications/MAMP/Library/bin/mysql When I start the IDE with a fresh userdir, only the latter is found and registered in the IDE, not the former.
You can always manually register the one you want. I don't know how we could fix this, if I changed the ordering the someone else would complain that /Applications/MAMP is not loaded.