Restoring single BSON file should use db set in URI

NSOptions in mongorestore have -d and -c options that are mirrored by the namespace options in mtc ToolOptions. Although the namespace options are normalized with the URI, the NSOptions are not. This leads to mongorestore not correctly detecting when a database has been set on the URI. We should refactor mongorestore to use the namespace options for database/collection instead of the NSOptions.