On Windows, connection profiles are stored in C:\Documents and Settings\UserName\Application Data\MySQL directory, where UserName is the name of the current Windows user. On Linux, the files are stored in the ~/.mysqlgui directory. The settings are stored in a file called mysqlx_user_connections.xml. The contents of that file look like this:

   <?xml version="1.0"?>
   <user_connections>
    <last_connection>1</last_connection>
    <password_storage_type>2</password_storage_type>
    <user_connection>
     <connection_name></connection_name>
     <username>root</username>
     <hostname>localhost</hostname>
     <port>3306</port>
     <schema></schema>
     <advanced_options/>
     <storage_path></storage_path>
     <notes></notes>
     <connection_type>0</connection_type>
     <storage_type>2</storage_type>
     <password></password>
    </user_connection>
    ...
  

You can edit the file manually, but take care not to invalidate the XML. When applying changes by editing and saving the file, those changes will show up the next time you open the Connections section of the Options Dialog. You do not need to restart your application for the changes to take effect.

As a database administrator, you may also edit the file according to your preferences, and then copy it to any other machine running the MySQL GUI tools. This makes it easy to have identical connection profiles on all machines, without having to set up those profiles individually. All XML configuration files for the MySQL GUI Tools are cross-platform compatible and can be transferred between Windows and Linux machines.