See this blog post for details. Prototype will eventually be removed from Jenkins core, and to prepare for this transition, this plugin must be migrated away from Prototype. The blog post contains instructions on how to find and eliminate usages of Prototype. In this plugin, the following usages of Prototype have been identified. This may not be an exhaustive list:

hudson/plugins/matrix_configuration_parameter/taglib/shortcut/shortcut.js:  e.observe("click", function(e) {
hudson/plugins/matrix_configuration_parameter/taglib/shortcut/shortcut.js:    var block = this.up(".matrix-combinations-parameter");