diff --git a/dvc/path/data_item.py b/dvc/path/data_item.py
index de93fe5ff..6a40c0ff1 100644
--- a/dvc/path/data_item.py
+++ b/dvc/path/data_item.py
@@ -1,4 +1,5 @@
 import os
+import stat
 import shutil
 
 from dvc.path.path import Path
@@ -104,6 +105,6 @@ class DataItem(object):
         md5 = file_md5(self.data.relative)[0]
         self._cache_file = os.path.join(self.cache_dir, md5)
         self._git.modify_gitignore([self.data.relative])
-        if os.path.isfile(self.cache.relative):
-            return
-        System.hardlink(self.data.relative, self.cache.relative)
+        if not os.path.isfile(self.cache.relative):
+            System.hardlink(self.data.relative, self.cache.relative)
+        os.chmod(self.data.relative, stat.S_IREAD)
diff --git a/dvc/path/factory.py b/dvc/path/factory.py
index efae5bf99..9dc3164fb 100644
--- a/dvc/path/factory.py
+++ b/dvc/path/factory.py
@@ -4,7 +4,7 @@ from dvc.path.data_item import DataItem, DataItemError, DataDirError
 from dvc.path.path import Path
 from dvc.path.stated_data_item import StatedDataItem
 from dvc.system import System
-
+from dvc.logger import Logger
 
 class PathFactory(object):
     def __init__(self, git, config):
diff --git a/dvc/repository_change.py b/dvc/repository_change.py
index c34916a92..f932b6554 100644
--- a/dvc/repository_change.py
+++ b/dvc/repository_change.py
@@ -7,7 +7,7 @@ from dvc.logger import Logger
 from dvc.path.data_item import DataDirError, DataItemInStatusDirError
 from dvc.path.stated_data_item import StatedDataItem
 from dvc.utils import cached_property
-
+from dvc.config import ConfigI
 
 class RepositoryChangeError(DvcException):
     def __init__(self, msg):
@@ -116,7 +116,10 @@ class RepositoryChange(object):
 
     def data_file_timesteps(self):
         res = set()
-        for root, dirs, files in os.walk('.'):
+        for root, dirs, files in os.walk(self._settings.git.git_dir_abs):
+            if root.startswith(os.path.join(self._settings.git.git_dir_abs, ConfigI.CONFIG_DIR)):
+                continue
+
             for file in files:
                 filename = os.path.join(root, file)
                 if os.path.exists(filename):