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Go to the Plugins Manager and verify that the modules that your project is using is marked as "Active". You may find that the needed modules are currently "Inactive".
In my case, the error message started appearing after an attempt to update my NetBeans 6.1 application. During the process, one of the modules failed to install properly. A warning appeared stating that additional modules failed to install due to the initial problem. After multiple cycles of updating NetBeans 6.1, the error message about the missing plug-ins persisted. After reviewing the "Installed" tab on the Plugins Manager and activating the needed modules, the error message went away.
Hope this helps.
Thanks for the reply. Your comment fixed the problem. In my case, I had JDK 1.6.0_07 automatically removed from my computer. I installed JDK 1.6.0_11 as per government requirements.
When I restarted to work on my TOMCAT webapp got the error: Unrecognized project: missing plug-in.
The fix was having the tomcat plugin installed.
Thanks for the help, but its interesting the JDK version is associated with Tomcat plugin. Maybe makes sense because TOMCAT uses JDK.