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When some code(mixed HTML & JSP) in a jsp-file is highlighted and toggle-comment is triggered, the html-comment type "<!-- -->" is used instead of the jsp comment-type "<%-- --%>" I think it was working with 6.8 but however it seems to be broken in 6.9. Maybe it has something to do with ticket #184005
This old bug may not be relevant anymore. If you can still reproduce it in 8.2 development builds please reopen this issue. Thanks for your cooperation, NetBeans IDE 8.2 Release Boss