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/utils/ndn-time.hpp b/utils/ndn-time.hpp
index d07c86e..7839f50 100644
--- a/utils/ndn-time.hpp
+++ b/utils/ndn-time.hpp
@@ -36,8 +36,8 @@
   std::string
   getSince() const;
 
-  boost::posix_time::time_duration
-  toPosixDuration(const system_clock::duration& duration) const;
+  system_clock::duration
+  toWaitDuration(system_clock::duration d) const;
 };
 
 class CustomSteadyClock : public CustomClock<steady_clock> {
@@ -48,8 +48,8 @@
   std::string
   getSince() const;
 
-  boost::posix_time::time_duration
-  toPosixDuration(const steady_clock::duration& duration) const;
+  steady_clock::duration
+  toWaitDuration(steady_clock::duration d) const;
 };
 
 } // namespace time