Git with multiple repositories is not working in Intellij IDEA Ultimate 2016

Does command line *git status* see all the changes correctly?

Are there any errors in the IDEA.log?

https://intellij-support.jetbrains.com/hc/en-us/articles/207241085

The *git status* along with all git commands (in git-bash.exe not in IDEA) works great!

IDEA log:

2017-04-05 18:22:28,712 [  54759]   INFO - tellij.vcs.log.data.VcsLogData - Username not configured for root file://D:/work/project/acme/acme-parent-pom
2017-04-05 18:22:30,887 [  56934]   INFO - tellij.vcs.log.data.VcsLogData - Username not configured for root file://D:/work/project/acme/acme-alpha-module
2017-04-05 18:22:32,075 [  58122]   INFO - tellij.vcs.log.data.VcsLogData - Username not configured for root file://D:/work/project/acme/acme-beta-module

Created a ticket #922316 to troubleshoot further

Also, git log contains following disappointing error :

2017-04-05 18:31:52,511 [ 618558]  ERROR - intellij.openapi.progress.Task - java.lang.IllegalStateException: The git operation should not fail in this context
java.lang.RuntimeException: java.lang.IllegalStateException: The git operation should not fail in this context
    at com.intellij.openapi.application.impl.LaterInvocator.invokeAndWait(LaterInvocator.java:189)
    at com.intellij.openapi.application.impl.ApplicationImpl.invokeAndWait(ApplicationImpl.java:655)
    at com.intellij.openapi.application.impl.ApplicationImpl.invokeAndWait(ApplicationImpl.java:660)
    at git4idea.merge.GitConflictResolver.showMergeDialog(GitConflictResolver.java:234)
    at git4idea.merge.GitConflictResolver.merge(GitConflictResolver.java:209)
    at git4idea.merge.GitConflictResolver.merge(GitConflictResolver.java:149)
    at git4idea.update.GitUpdateProcess.areUnmergedFiles(GitUpdateProcess.java:370)
    at git4idea.update.GitUpdateProcess.update(GitUpdateProcess.java:118)
    at git4idea.update.GitUpdateEnvironment.updateDirectories(GitUpdateEnvironment.java:60)
    at com.intellij.openapi.vcs.update.AbstractCommonUpdateAction$Updater.a(AbstractCommonUpdateAction.java:354)
    at com.intellij.openapi.vcs.update.AbstractCommonUpdateAction$Updater.run(AbstractCommonUpdateAction.java:330)
    at com.intellij.openapi.progress.impl.CoreProgressManager$TaskRunnable.run(CoreProgressManager.java:710)
    at com.intellij.openapi.progress.impl.CoreProgressManager$3.run(CoreProgressManager.java:179)
    at com.intellij.openapi.progress.impl.CoreProgressManager.a(CoreProgressManager.java:568)
    at com.intellij.openapi.progress.impl.CoreProgressManager.executeProcessUnderProgress(CoreProgressManager.java:519)
    at com.intellij.openapi.progress.impl.ProgressManagerImpl.executeProcessUnderProgress(ProgressManagerImpl.java:54)
    at com.intellij.openapi.progress.impl.CoreProgressManager.runProcess(CoreProgressManager.java:164)
    at com.intellij.openapi.progress.impl.ProgressManagerImpl$1.run(ProgressManagerImpl.java:128)
    at com.intellij.openapi.application.impl.ApplicationImpl$2.run(ApplicationImpl.java:309)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.IllegalStateException: The git operation should not fail in this context
    at git4idea.merge.GitMergeProvider$MyMergeSession.<init>(GitMergeProvider.java:481)
    at git4idea.merge.GitMergeProvider.createMergeSession(GitMergeProvider.java:400)
    at com.intellij.openapi.vcs.merge.MultipleFileMergeDialog.<init>(MultipleFileMergeDialog.java:153)
    at com.intellij.openapi.vcs.impl.AbstractVcsHelperImpl.showMergeDialog(AbstractVcsHelperImpl.java:620)
    at git4idea.merge.GitConflictResolver.lambda$showMergeDialog$0(GitConflictResolver.java:236)
    at com.intellij.openapi.application.TransactionGuardImpl$6.run(TransactionGuardImpl.java:318)
    at com.intellij.openapi.application.impl.LaterInvocator$1.run(LaterInvocator.java:166)
    at com.intellij.openapi.application.impl.LaterInvocator$FlushQueue.a(LaterInvocator.java:417)
    at com.intellij.openapi.application.impl.LaterInvocator$FlushQueue.run(LaterInvocator.java:401)
    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:80)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
    at com.intellij.ide.IdeEventQueue.c(IdeEventQueue.java:843)
    at com.intellij.ide.IdeEventQueue._dispatchEvent(IdeEventQueue.java:679)
    at com.intellij.ide.IdeEventQueue.dispatchEvent(IdeEventQueue.java:391)
    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: com.intellij.openapi.vcs.VcsException: The file D:/work/project/acme/acme-beta-module is not under Git
    at git4idea.GitUtil.sortFilesByGitRoot(GitUtil.java:239)
    at git4idea.GitUtil.sortFilesByGitRoot(GitUtil.java:217)
    at git4idea.merge.GitMergeProvider$MyMergeSession.<init>(GitMergeProvider.java:428)
    ... 25 more

PS: needless to say, I added all modules under Git in the Settings -> Version Control  as I mentioned in my first post.