Refactored IOException to be taken out as early as possible. This might cause some null pointer exceptions that need to be taken care of. Part of study variable and study variables repository operations finished with many of the remaining sketched out.
Huge refactoring to the way database data is requested. Now errors are caught earlier and travel through the program. Many error messages are logged through Logger which still needs to be configured to write in file instead of standard output. TransferData (replacement for transfer objects) has been fleshed out but actual usage is still to be done.
Solved merge conflicts.