Removed dependencies in check.settings

* The first commit sets default settings for the database if settings$database is null
* The second commit removes dependencies on 1) a database connection, 2) a model, and 3) a run. 

The goal of these changes is to make PEcAn more modular - e.g. if someone wants to just do the meta-analysis, model and run information should not be strictly required. But please let me know if I am missing something important.