See this blog post for details. Prototype will eventually be removed from Jenkins core. 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:
./src/main/webapp/scripts/webapp.js:12: $(radios).each(function (radio) {
./src/main/webapp/scripts/webapp.js:19: e = $(e).next();
./src/main/webapp/scripts/webapp.js:20: if (Element.hasClassName(e, "radio-block-start"))
./src/main/webapp/scripts/webapp.js:22: if (Element.hasClassName(e, "radio-block-end"))
./src/main/webapp/scripts/webapp.js:42: n = n.next();
./src/main/webapp/scripts/webapp.js:130: new Ajax.Request(checkLinuxUrl, config);
[{"id":-1,"name":"My open issues","jql":"assignee = currentUser() AND resolution = Unresolved order by updated DESC","isSystem":true,"sharePermissions":[],"requiresLogin":true},{"id":-2,"name":"Reported by me","jql":"reporter = currentUser() order by created DESC","isSystem":true,"sharePermissions":[],"requiresLogin":true},{"id":-4,"name":"All issues","jql":"order by created DESC","isSystem":true,"sharePermissions":[],"requiresLogin":false},{"id":-5,"name":"Open issues","jql":"resolution = Unresolved order by priority DESC,updated DESC","isSystem":true,"sharePermissions":[],"requiresLogin":false},{"id":-9,"name":"Done issues","jql":"statusCategory = Done order by updated DESC","isSystem":true,"sharePermissions":[],"requiresLogin":false},{"id":-3,"name":"Viewed recently","jql":"issuekey in issueHistory() order by lastViewed DESC","isSystem":true,"sharePermissions":[],"requiresLogin":false},{"id":-6,"name":"Created recently","jql":"created >= -1w order by created DESC","isSystem":true,"sharePermissions":[],"requiresLogin":false},{"id":-7,"name":"Resolved recently","jql":"resolutiondate >= -1w order by updated DESC","isSystem":true,"sharePermissions":[],"requiresLogin":false},{"id":-8,"name":"Updated recently","jql":"updated >= -1w order by updated DESC","isSystem":true,"sharePermissions":[],"requiresLogin":false}]
zooopx FYI