Fix metadata reshaping when time dim is implicit and the split file dim array has time as a dimension

Finish metadata reshaping for retrieve = TRUE, including different combinations of merge_across_dims, merge_across_dims_narm, and split_multiselected_dims

Change function chunk_indices() to get_chunk_indices() because chunk_indices is an item in some functions

Start() can correctly merge files along the dimension that has different length each file, without additional NAs.

Deprecate 'crop' in CDORemapper() and add variable 'crop_domain' for automatically generating 'crop'

Deprecate 'crop' in CDORemapper(). It is automatically assigned as the borders of lat/lon selectors in Start() call. (WIP)