[Issue#81]: Fix for structure that were identified as functions passing vault and using new is_call_to_functions.

Reformulated is_call_to_function to use the vault information in our advantage. Now we need to pass the current routine as an argument to calls_to_functions.

Bugfixes to fix issues that appeared when including the sea-ice. Changes include: - Fix in calls_to_functions, dimension of contents, has_operations and calls_to_procedure.

Added a new command line "--additional-source" argument which can be used to apply the changes that are necessary to the preprocessed files also to a different source directory. It will allow to automatically transfer last minute fixes directly to the original source.