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I had a NB 3.6 installation (A) which was configured with one separate Tomcat installation in addition to the built in server. I then wanted to run 3.6 with SASPE 8, so I downloaded the bundle from java.sun.com. Unfortunately, this meant that I had to install a new version of 3.6 (B). I ran that B and tried to execute somethings on the appserver. When I started it, it took my settings from installation A. I quit B and started A. I note that A does not include the appserver as an option (to be expected, since it doesn't have the plugin). I went to the runtime tab to configure one of the Tomcats as my default server, and I got an invocationtarget exception in doing so (see attachment). [BTW, I don't want two 3.6 installations anyway - shouldn't the bundle configure the existing one, and/or remove it, instead of just setting up a second version - there is bound to be problems with this scenario. And many people who go for the bundle will have the regular release installed.]
What you can do from a pure NetBeans 3.6 installation is go to update Center and install the as8 plugin as an extra plugin, without using the Cobundle installer.
Created attachment 15641 [details] Stack trace
I try to deploy my application but it fails. I get a really cryptic message dialog. "Deployment error: Failed to lookup configuration for Tomcat5in . See ide log for ..." (I think you forgot to wrap the error messages in this dialog, will file a separate issue for this). I will attach the message from the ide.log. It seems like the IDE has become unusable at this point. I confirmed it by restarting: yep, I get an InvocationTargetException on startup, and I cannot deploy after restarting the IDE either.
Created attachment 15642 [details] extract from the ide.log
Note that there are more bugs with the some synopsis: #43404, #43602. I remember I had the some problem even without the appserver plugin.
Having two installations of IDE with different sets of module share the same userdir is not supported. As Ludo suggested use update center for AS plugin or at least use 2 different use directories. The first exception appears to be caused by presence of server settings w/o the corresponding plugin. The rest appears to be duplicate of #43602 as Marek noted. *** This issue has been marked as a duplicate of 43602 ***