security+node: Fixing includes and removing deprecated files

Change-Id: If1565b8ae9c1c1dd78a0bc0490c76a836c1ceacf
diff --git a/src/security/certificate/certificate.cpp b/src/security/certificate/certificate.cpp
index 7a70cdc..414785d 100644
--- a/src/security/certificate/certificate.cpp
+++ b/src/security/certificate/certificate.cpp
@@ -8,7 +8,7 @@
 
 #include <ndn-cpp/common.hpp>
 
-#include "certificate.hpp"
+#include <ndn-cpp/security/certificate/certificate.hpp>
 
 #if NDN_CPP_USE_SYSTEM_BOOST
 #include <boost/iostreams/stream.hpp>