security: Reorganizing source code to prepare for support of two version of NDN certificates

This commit also removes unused ndn_digestSha256 function and deprecates
crypto::sha256 in favor of crypto::computeSha256Digest in util/crypto.hpp.

Change-Id: I24ee50ff073a96b868633bdf2cfade412d3605f3
Refs: #3098
diff --git a/.waf-tools/cryptopp.py b/.waf-tools/cryptopp.py
index 4035693..1632ab6 100644
--- a/.waf-tools/cryptopp.py
+++ b/.waf-tools/cryptopp.py
@@ -27,7 +27,7 @@
 CRYPTOPP_VERSION_FILE = 'config.h'
 
 CRYPTOPP_CHECK_FRAGMENT = '''
-#include "../../src/security/cryptopp.hpp"
+#include "../../src/security/v1/cryptopp.hpp"
 #include <iostream>
 
 int