Break up CuBIDS class into functions as much as possible

[tsalo]

I find testing methods within the CuBIDS class difficult because they all rely so much on the actual class, which requires a lot of stuff (e.g., code directory, dataset), so it would be great to do an audit of the methods of the CuBIDS class to see what can be split out into separate functions.

[mattcieslak]

I completely agree, it's super cumbersome and I get nervous every time i see link numbers in the thousands. Also, the class attributes are not well-explained anywhere and it would be easier/clearer to document them as inputs to standalone functions

[tsalo]

At minimum, I think the Datalad methods (init_datalad, datalad_save, is_datalad_clean, datalad_undo_last_commit) could be moved into their own class or separate functions.