Rearranged the packet and serial code to make more sense

This mostly just reimplements the best parts of the discarded branch:

> discard-encapsulated-packets

There may still be some work needed.

server/server_logic.cpp

@@ -21,9 +21,6 @@
 */
 #include "server_application.hpp"
 
-//for PACKET_BUFFER_SIZE
-#include "serial.hpp"
-
 //utility functions
 #include "sql_utility.hpp"
 #include "utility.hpp"