Stack dump of thread which is refreshing the project:

java.net.URI$Parser.charAt(URI.java:2837)
java.net.URI$Parser.at(URI.java:2843)
java.net.URI$Parser.parse(URI.java:3013)
java.net.URI.<init>(URI.java:663)
java.net.URI.<init>(URI.java:764)
org.eclipse.core.filesystem.URIUtil.toURI(URIUtil.java:133)
org.eclipse.core.filesystem.URIUtil.toURI(URIUtil.java:95)
org.eclipse.core.internal.filesystem.local.LocalFile.toURI(LocalFile.java:425)
org.eclipse.core.internal.resources.AliasManager$1.compare(AliasManager.java:485)
java.util.TreeMap.getEntryUsingComparator(TreeMap.java:351)
java.util.TreeMap.getEntry(TreeMap.java:322)
java.util.TreeMap.get(TreeMap.java:255)
org.eclipse.core.internal.resources.AliasManager$LocationMap.matchingResourcesDo(AliasManager.java:193)
org.eclipse.core.internal.resources.AliasManager.internalComputeAliases(AliasManager.java:605)
org.eclipse.core.internal.resources.AliasManager.computeAliases(AliasManager.java:427)
org.eclipse.core.internal.localstore.RefreshLocalAliasVisitor.createResource(RefreshLocalAliasVisitor.java:34)
org.eclipse.core.internal.localstore.RefreshLocalVisitor.synchronizeExistence(RefreshLocalVisitor.java:216)
org.eclipse.core.internal.localstore.RefreshLocalVisitor.visit(RefreshLocalVisitor.java:290)
org.eclipse.core.internal.localstore.UnifiedTree.accept(UnifiedTree.java:99)
org.eclipse.core.internal.localstore.FileSystemResourceManager.refreshResource(FileSystemResourceManager.java:739)
org.eclipse.core.internal.localstore.FileSystemResourceManager.refresh(FileSystemResourceManager.java:723)
org.eclipse.core.internal.resources.Resource.refreshLocal(Resource.java:1476)
org.eclipse.core.internal.resources.Resource.createLink(Resource.java:619)
org.eclipse.core.internal.resources.Project.reconcileLinks(Project.java:966)
org.eclipse.core.internal.resources.Project.open(Project.java:876)
org.eclipse.core.internal.resources.Project.open(Project.java:911)
org.eclipse.jdt.internal.core.ExternalFoldersManager.createExternalFoldersProject(ExternalFoldersManager.java:153)
org.eclipse.jdt.internal.core.ExternalFoldersManager.createLinkFolder(ExternalFoldersManager.java:108)
org.eclipse.jdt.internal.core.ExternalFolderChange.updateExternalFoldersIfNecessary(ExternalFolderChange.java:47)
org.eclipse.jdt.internal.core.DeltaProcessor.resourceChanged(DeltaProcessor.java:1956)
org.eclipse.jdt.internal.core.DeltaProcessingState.resourceChanged(DeltaProcessingState.java:410)
org.eclipse.core.internal.events.NotificationManager$2.run(NotificationManager.java:288)
org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:37)
org.eclipse.core.internal.events.NotificationManager.notify(NotificationManager.java:282)
org.eclipse.core.internal.events.NotificationManager.broadcastChanges(NotificationManager.java:148)
org.eclipse.core.internal.resources.Workspace.broadcastBuildEvent(Workspace.java:297)
org.eclipse.core.internal.events.AutoBuildJob.doBuild(AutoBuildJob.java:136)
org.eclipse.core.internal.events.AutoBuildJob.run(AutoBuildJob.java:238)
org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)