Upgrade the underlying NFD and ndn-cxx to version 0.6.1 and fixing compilation

Specific changes:

1) model: NetDeviceTransport uses the MTU of NS-3 netDevice
2) utils: Adapting to the updates of the ndn-cxx CustomClock abstraction

Change-Id: Ic0dba06a9afd66a810172d4a512f35f6df6b222a
Refs: #4471, #4514
diff --git a/.gitmodules b/.gitmodules
index eda145d..fb3347b 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,6 +1,8 @@
 [submodule "NFD"]
 	path = NFD
 	url = https://github.com/named-data-ndnSIM/NFD
+	branch = NFD-0.6.1-ndnSIM
 [submodule "ndn-cxx"]
 	path = ndn-cxx
 	url = https://github.com/named-data-ndnSIM/ndn-cxx
+	branch = ndn-cxx-0.6.1-ndnSIM