dvc init fails if repository has files marked with --skip-worktree
Using dvc 0.9.3, running `dvc init` will yield `Unexpected Error: ` (but creates the `.dvc` directory anyway).

Observed in Python 3.6 on Windows and Python 3.5 on WSL (Ubuntu) - both installed from PyPI.
diff --git a/dvc/scm.py b/dvc/scm.py
index 34d11d444..ecced4059 100644
--- a/dvc/scm.py
+++ b/dvc/scm.py
@@ -1,6 +1,7 @@
 import os
 
 from dvc.exceptions import DvcException
+from dvc.logger import Logger
 
 
 class SCMError(DvcException):
@@ -131,7 +132,14 @@ class Git(Base):
             fd.writelines(filtered)
 
     def add(self, paths):
-        self.repo.index.add(paths)
+        # NOTE: GitPython is not currently able to handle index version >= 3.
+        # See https://github.com/iterative/dvc/issues/610 for more details.
+        try:
+            self.repo.index.add(paths)
+        except AssertionError as exc:
+            msg = 'Failed to add \\'{}\\' to git. You can add those files manually using \\'git add\\'. '
+            msg += 'See \\'https://github.com/iterative/dvc/issues/610\\' for more details.'
+            Logger.error(msg.format(str(paths)), exc)
 
     def commit(self, msg):
         self.repo.index.commit(msg)
['dvc/scm.py']