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After upgrade from 1.5.8 to 1.6.3 I was got this result when running refreshLinks.php:

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A database error has occurred
Query: SELECT page_namespace,page_title,page_id  FROM `mw_page`,`mw_templatelink
s`  WHERE (tl_from=page_id) AND tl_namespace = '0' AND tl_title = 'Заглавная_страница'
Function: Title::getLinksTo
Error: 1267 Illegal mix of collations (latin1_bin,IMPLICIT) and (utf8_general_ci
,COERCIBLE) for operation '=' (localhost)
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Problem was resolved with changing tl_title type from

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CREATE TABLE /*$wgDBprefix*/templatelinks (
  tl_from int(8) unsigned NOT NULL default '0',

  -- Key to page_namespace/page_title of the target page.
  -- The target page may or may not exist, and due to renames
  -- and deletions may refer to different page records as time
  -- goes by.
  tl_namespace int NOT NULL default '0',
  tl_title varchar(255) binary NOT NULL default '',

  UNIQUE KEY tl_from(tl_from,tl_namespace,tl_title),
  KEY (tl_namespace,tl_title)

) TYPE=InnoDB;
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to

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CREATE TABLE `mw_templatelinks` (
  `tl_from` int(8) unsigned NOT NULL default '0',
  `tl_namespace` int(11) NOT NULL default '0',
  `tl_title` varchar(255) character set utf8 collate utf8_bin NOT NULL default '',
  UNIQUE KEY `tl_from` (`tl_from`,`tl_namespace`,`tl_title`),
  KEY `tl_namespace` (`tl_namespace`,`tl_title`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8;
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