Use FileUtils.rmdir instead of rm -rf

This prevents accidentally deletion of untracked files in the submodule
and is cross-platform compatible.

Author: sds

lib/overcommit/hook_context/pre_commit.rb

@@ -137,7 +137,7 @@ def clear_working_tree
       # Work around this by removing these empty submodule directories as there
       # doesn't appear any reason to keep them around.
       removed_submodules.each do |submodule|
-        `rm -rf #{submodule.path}`
+        FileUtils.rmdir(submodule.path)
       end
     end