The exception might have been introduced during one of the bug fixes.
For solving this you might need to check each and every commit on IGB codebase.

Exception:
Exception in thread "AWT-EventQueue-0" java.lang.NoClassDefFoundError: org/lorainelab/igb/plugin/manager/ResourceWrapper
at org.lorainelab.igb.plugin.manager.BundleInfoManager.getFilteredRepositoryBundles(BundleInfoManager.java:116)
at org.lorainelab.igb.plugin.manager.BundleInfoManager.refreshBundleInfo(BundleInfoManager.java:71)
at org.lorainelab.igb.plugin.manager.BundleInfoManager.reloadRepositoryBundles(BundleInfoManager.java:106)
at org.lorainelab.igb.plugin.manager.RepositoryInfoManager$1.finished(RepositoryInfoManager.java:76)
at com.affymetrix.genometry.thread.CThreadWorker.done(CThreadWorker.java:51)
at javax.swing.SwingWorker$5.run(SwingWorker.java:737)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:832)
at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:112)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:842)
at javax.swing.Timer.fireActionPerformed(Timer.java:313)
at javax.swing.Timer$DoPostEvent.run(Timer.java:245)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.ClassNotFoundException: Unable to load class 'org.lorainelab.igb.plugin.manager.ResourceWrapper' because the bundle wiring for org.lorainelab.igb.plugins-manager is no longer valid.
at org.apache.felix.framework.BundleWiringImpl.findClassOrResourceByDelegation(BundleWiringImpl.java:1523)
at org.apache.felix.framework.BundleWiringImpl.access$400(BundleWiringImpl.java:79)
at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.loadClass(BundleWiringImpl.java:1998)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 25 more
Exception in thread "AWT-EventQueue-0" java.lang.NoClassDefFoundError: org/lorainelab/igb/plugin/manager/ResourceWrapper
at org.lorainelab.igb.plugin.manager.BundleInfoManager.getFilteredRepositoryBundles(BundleInfoManager.java:116)
at org.lorainelab.igb.plugin.manager.BundleInfoManager.refreshBundleInfo(BundleInfoManager.java:71)
at org.lorainelab.igb.plugin.manager.BundleInfoManager.reloadRepositoryBundles(BundleInfoManager.java:106)
at org.lorainelab.igb.plugin.manager.RepositoryInfoManager$1.finished(RepositoryInfoManager.java:76)
at com.affymetrix.genometry.thread.CThreadWorker.done(CThreadWorker.java:51)
at javax.swing.SwingWorker$5.run(SwingWorker.java:737)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:832)
at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:112)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:842)
at javax.swing.Timer.fireActionPerformed(Timer.java:313)
at javax.swing.Timer$DoPostEvent.run(Timer.java:245)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)