I was stumped by a problem like this the other day and it turned out I had a method breakpoint somewhere by accident which causes the VM to slow down massively. First double check you don't have a stray breakpoint somewhere using the breakpoint manager in your IDE.
Geneious from dev-kit launch hangs at iseek.license.ag.run
I've been following the phobos plugin tutorial and things were working, but now Geneious hangs unexpectedly. I am using the 9.0.4 devkit with IntelliJ 15.0.1 on Ubuntu 15.10. I followed the setup.html instructions and was able to test the setup with the 'ExampleDocumentViewerPlugin' and set a breakpoint in the paintComponent method. I then started on the phobos tutorial and was able to copy the 'ExampleAnnotationSequenceGenerator' module with the build file (although I had to make some changes to deal with the two 32 and 64 bit run configuration files).
I then started working through the tutorial and called Geneious successfully several times with the debug command. However, when I tried today, Geneious will launch with the debug command, but as soon as I click on a document, it becomes unresponsive. The console shows Geneious hung at com.biomatters.iseek.license.ag.run. Not sure if this matters, but my main installation is using a trial license.
I also tried to use the build.xml to export the partially-finished phobos plugin as a folder, and copied that folder into my normal Geneious bundledPlugins folder. My normal Geneious started just fine and the plugin was available (although it doesn't really do anything yet).
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Yeah, no breakpoints, but I figured out the problem. I was using JDK7, switched it over to JDK6 and things are working again. Wow that was frustrating...I had seen that v9 doesn't use Java 6 any more, and I only had JDK7 installed, so I gave it a try. It worked perfectly and that was less than 2 weeks ago, so I didn't even think to download and test JDK6. Well I guess there must have been some sort of update, because switching the project over to JDK6 did the trick. Now please excuse me while I go repair the head sized hole in my apartment wall....
OK, glad you got it working. For R9 we recommend compiling the project with the latest JDK6 and running Geneious with Java 8 update 60 or later. That's what we use.