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Steps to reproduce:
1) Clone a git repo that has git submodules.
2) Don't init the submodules. (This is not a step you must do, but a step you shouldn't do ;) )
3) Open solution in MD.
4) Do some code change in the repo.
5) Right-click on solution -> Version Control -> Review changes.
The submodule shows up with a "Delete" status.
Submodule should not show up, since no changes were made to it.
Oh, just realised that this may be a dupe of bug 3823.
*** This bug has been marked as a duplicate of bug 3823 ***
Given that bug 3823 has been marked as NORESPONSE, when the steps to reproduce here still show a bug, then I'm reopening this bug (because I have no permissions to reopen bug 3823).
Fixed in libgit2 branch.