!MESSAGE Authorization infrastructure (org.eclipse.core.runtime.compatibility.auth) not installed.
!STACK 0
java.lang.ClassNotFoundException: org.eclipse.core.internal.runtime.auth.AuthorizationDatabase cannot be found by org.eclipse.core.runtime_3.12.0.v20160920-1429
	at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:461)
	at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:372)
	at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:364)
	at org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:161)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Class.java:264)
	at org.eclipse.core.internal.runtime.AuthorizationHandler.getAuthClass(AuthorizationHandler.java:48)
	at org.eclipse.core.internal.runtime.AuthorizationHandler.loadKeyring(AuthorizationHandler.java:69)
	at org.eclipse.core.internal.runtime.AuthorizationHandler.flushAuthorizationInfo(AuthorizationHandler.java:231)
	at org.eclipse.core.runtime.Platform.flushAuthorizationInfo(Platform.java:590)
	at com.atlassian.connector.eclipse.internal.commons.ui.MigrateToSecureStorageJob.migrateToSecureStorage(MigrateToSecureStorageJob.java:89)
	at com.atlassian.connector.eclipse.internal.commons.ui.MigrateToSecureStorageJob.runInUIThread(MigrateToSecureStorageJob.java:60)

!ENTRY org.eclipse.core.jobs 4 2 2016-11-17 21:09:30.244
!MESSAGE An internal error occurred during: "Start Embedded Web Server".
!STACK 0
java.lang.LinkageError: loader constraint violation: when resolving method "org.mortbay.jetty.servlet.ServletHolder.<init>(Ljavax/servlet/Servlet;)V" the class loader (instance of org/eclipse/osgi/internal/loader/EquinoxClassLoader) of the current class, com/atlassian/connector/eclipse/internal/directclickthrough/ui/DirectClickThroughUiPlugin$2, and the class loader (instance of org/eclipse/osgi/internal/loader/EquinoxClassLoader) for the method's defining class, org/mortbay/jetty/servlet/ServletHolder, have different Class objects for the type javax/servlet/Servlet used in the signature
	at com.atlassian.connector.eclipse.internal.directclickthrough.ui.DirectClickThroughUiPlugin$2.runImpl(DirectClickThroughUiPlugin.java:88)
	at com.atlassian.connector.eclipse.internal.core.jobs.JobWithStatus.run(JobWithStatus.java:50)
	at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)


depends on and installs javax.servlet:

* com.atlassian.connector.eclipse.bamboo.feature
* com.atlassian.connector.eclipse.directclickthrough.feature
* com.atlassian.connector.eclipse.jira.feature
* com.atlassian.connector.commons.feature -> connector.commons -> javax.xml.rpc 1.1.0 -> javax.servlet 3.1.0