Update write/read Bbox to include padding values

[arezaii]

The current bbox file text only includes point and extent values.

Padding values are needed in order to properly locate a domain inside the larger CONUS model.

• Update the read_bbox and write_bbox functions to include the padding values
• Update read_bbox to return a proper Bbox object
• Update write bbox to accept a proper Bbox object
• Update associated classes that use plain array style bboxes
• Update tests for read_bbox, write_bbox, associated classes