checked out some file located in package a.b it appears in the changes view delete package a now, shedule it for deleting from CC: now both package ans file are shown in Changes view. Refresh helps, but if you don't refresh, then the changes committing/rolling back cause exceptions: Rollback: No message java.lang.NullPointerException at net.sourceforge.transparent.TransparentVcs.undoCheckoutFile(TransparentVcs.java:638) at net.sourceforge.transparent.CCaseCheckinEnvironment.rollbackChanged(CCaseCheckinEnvironment.java:475) at net.sourceforge.transparent.CCaseCheckinEnvironment.rollbackChanges(CCaseCheckinEnvironment.java:345) at com.intellij.openapi.vcs.changes.ui.RollbackChangesDialog$1$1.process(RollbackChangesDialog.java:8) at com.intellij.openapi.vcs.changes.ChangesUtil.processItemsByVcs(ChangesUtil.java:132) at com.intellij.openapi.vcs.changes.ChangesUtil.processChangesByVcs(ChangesUtil.java:137) at com.intellij.openapi.vcs.changes.ui.RollbackChangesDialog$1.run(RollbackChangesDialog.java:1) at com.intellij.openapi.progress.impl.ProgressManagerImpl$2.run(ProgressManagerImpl.java:4) at com.intellij.openapi.progress.impl.ProgressManagerImpl.executeProcessUnderProgress(ProgressManagerImpl.java:41) at com.intellij.openapi.progress.impl.ProgressManagerImpl.runProcess(ProgressManagerImpl.java:51) at com.intellij.openapi.application.impl.ApplicationImpl$6$1.run(ApplicationImpl.java:4) at com.intellij.openapi.application.impl.ApplicationImpl$4.run(ApplicationImpl.java:7) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269) at java.util.concurrent.FutureTask.run(FutureTask.java:123) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675) at java.lang.Thread.run(Thread.java:595) at com.intellij.openapi.application.impl.ApplicationImpl$1$1.run(ApplicationImpl.java:3) Commit: No message java.lang.NullPointerException at com.intellij.openapi.vcs.changes.ChangeListManagerImpl.getChange(ChangeListManagerImpl.java:376) at net.sourceforge.transparent.CCaseCheckinEnvironment.getChangeListName(CCaseCheckinEnvironment.java:678) at net.sourceforge.transparent.CCaseCheckinEnvironment.commitChanged(CCaseCheckinEnvironment.java:322) at net.sourceforge.transparent.CCaseCheckinEnvironment.commit(CCaseCheckinEnvironment.java:144) at com.intellij.openapi.vcs.changes.ui.CommitHelper$4.process(CommitHelper.java:9) at com.intellij.openapi.vcs.changes.ChangesUtil.processItemsByVcs(ChangesUtil.java:132) at com.intellij.openapi.vcs.changes.ChangesUtil.processChangesByVcs(ChangesUtil.java:137) at com.intellij.openapi.vcs.changes.ui.CommitHelper.b(CommitHelper.java:64) at com.intellij.openapi.vcs.changes.ui.CommitHelper.access$100(CommitHelper.java:18) at com.intellij.openapi.vcs.changes.ui.CommitHelper$2.run(CommitHelper.java:1) at com.intellij.openapi.vcs.changes.ui.CommitHelper$1.run(CommitHelper.java:6) at com.intellij.openapi.progress.impl.ProgressManagerImpl$4.run(ProgressManagerImpl.java:4) at com.intellij.openapi.progress.impl.ProgressManagerImpl$5.run(ProgressManagerImpl.java:1) at com.intellij.openapi.progress.impl.ProgressManagerImpl$2.run(ProgressManagerImpl.java:4) at com.intellij.openapi.progress.impl.ProgressManagerImpl.executeProcessUnderProgress(ProgressManagerImpl.java:41) at com.intellij.openapi.progress.impl.ProgressManagerImpl.runProcess(ProgressManagerImpl.java:51) at com.intellij.openapi.progress.impl.ProgressManagerImpl$6.run(ProgressManagerImpl.java:2) at com.intellij.openapi.application.impl.ApplicationImpl$4.run(ApplicationImpl.java:7) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269) at java.util.concurrent.FutureTask.run(FutureTask.java:123) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675) at java.lang.Thread.run(Thread.java:595) at com.intellij.openapi.application.impl.ApplicationImpl$1$1.run(ApplicationImpl.java:3)