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/model/ndn-net-device-transport.cpp b/model/ndn-net-device-transport.cpp
index 2d946c8..32abaa6 100644
--- a/model/ndn-net-device-transport.cpp
+++ b/model/ndn-net-device-transport.cpp
@@ -47,7 +47,7 @@
   this->setScope(scope);
   this->setPersistency(persistency);
   this->setLinkType(linkType);
-  // this->setMtu(udp::computeMtu(m_socket.local_endpoint())); // not sure what should be here
+  this->setMtu(m_netDevice->GetMtu()); // Use the MTU of the netDevice
 
   NS_LOG_FUNCTION(this << "Creating an ndnSIM transport instance for netDevice with URI"
                   << this->getLocalUri());