Moving apps back to apps/ folder.  Finally worked out the problem with headers

WAF building system copies all headers to one directory. As a result,
all #include directives in all NS3 modules should be either in form
"ns3/header-file.h" or just "header-file.h", disregarding the actual
directory structure.
diff --git a/model/ndnabstraction-header.h b/model/ndnabstraction-header.h
index 7d652ff..2cbd4a3 100644
--- a/model/ndnabstraction-header.h
+++ b/model/ndnabstraction-header.h
@@ -23,6 +23,7 @@
 
 #include <stdint.h>
 #include <vector>
+
 #include "ns3/header.h"
 #include "ns3/ipv4-address.h"
 #include "ns3/nstime.h"