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The SHOW VARIABLES LIKE .../SELECT @@/SELECT ... FROM INFORMATION_SCHEMA.VARIABLES were assuming that all the system variables are in system charset (UTF-8). However the variables that are settable through command line will have a different character set (character_set_filesystem). Fixed the server to remember the correct character set of basedir, datadir, tmpdir, ssl, plugin_dir, slave_load_tmpdir, innodb variables; init_connect and init_slave variables and use it when processing data.
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