After several weeks of negotiations with team president Paul Dolan, Mark Shapiro and the Indians have agreed to a five-year contract extension through the 2012 season. The agreement was officially announced by the club Thursday. Shapiro, 39, is entering his 16th season with the Indians organization and his sixth as the executive vice president and GM. His tenure, to this point, has been defined by the rebuilding of the big-league club that he orchestrated beginning in 2002.