restructure external code and handle 3rd party licenses correctly

core/src/NameHierarchy.cpp

@@ -16,7 +16,7 @@
 
 #include "NameHierarchy.h"
 
-#include "json/json.hpp"
+#include "json.hpp"
 
 namespace sourcetrail
 {

core/src/SourcetrailDBWriter.cpp

@@ -20,7 +20,7 @@
 #include <fstream>
 #include <vector>
 
-#include "sqlite/CppSQLite3.h"
+#include "CppSQLite3.h"
 
 #include "DatabaseStorage.h"
 #include "DefinitionKind.h"