• consider project with 2 modules: 1-st module's content root is project root, 2-nd module is located in 'nestedModule' subfolder of project directory. The 'nestedModule' directory is excluded in 1-st module. For each module conten root separate vss mapping is configured:
  1) project_dir === $/myproject/
  2) project_dir/nestedModule === $/myproject/nestedModule/

• both modules contain package named for example 'aaa'. Invoke Rename for one of the packages: both packages are to be renamed; classes from both packages are checked out; but the only 1 package (from 1st module) appears in Changes view.
• commit: teh changeslist is committed, but now the checked out files from second package are recognized as not committed. They appear in Changes view, but their package change is not recognized yet, so on attempt to commit the change exception is thrown.

The problem completely goes away if you refresh the Changes view before first commit.

No message
java.lang.NullPointerException
at com.intellij.vcsUtil.VcsUtil.isRenameChange(VcsUtil.java:347)
at com.intellij.vssSupport.Checkin.VssCheckinEnvironment.commitRenamedFolders(VssCheckinEnvironment.java:183)
at com.intellij.vssSupport.Checkin.VssCheckinEnvironment.commit(VssCheckinEnvironment.java:147)
at com.intellij.openapi.vcs.changes.ui.CommitHelper$4.process(CommitHelper.java:137)
at com.intellij.openapi.vcs.changes.ChangesUtil.processItemsByVcs(ChangesUtil.java:236)
at com.intellij.openapi.vcs.changes.ChangesUtil.processChangesByVcs(ChangesUtil.java:241)
at com.intellij.openapi.vcs.changes.ui.CommitHelper.performCommit(CommitHelper.java:131)
at com.intellij.openapi.vcs.changes.ui.CommitHelper.access$100(CommitHelper.java:31)
at com.intellij.openapi.vcs.changes.ui.CommitHelper$2.run(CommitHelper.java:116)
at com.intellij.openapi.vcs.changes.ui.CommitHelper$1.run(CommitHelper.java:83)
at com.intellij.openapi.progress.impl.ProgressManagerImpl$5.run(ProgressManagerImpl.java:238)
at com.intellij.openapi.progress.impl.ProgressManagerImpl$2.run(ProgressManagerImpl.java:128)
at com.intellij.openapi.progress.impl.ProgressManagerImpl.executeProcessUnderProgress(ProgressManagerImpl.java:149)
at com.intellij.openapi.progress.impl.ProgressManagerImpl.runProcess(ProgressManagerImpl.java:119)
at com.intellij.openapi.progress.impl.ProgressManagerImpl$6.run(ProgressManagerImpl.java:246)
at com.intellij.openapi.application.impl.ApplicationImpl$5.run(ApplicationImpl.java:297)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:885)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
at java.lang.Thread.run(Thread.java:619)
at com.intellij.openapi.application.impl.ApplicationImpl$1$1.run(ApplicationImpl.java:106)