Still using `partial_fill` when creating FileTreeQuery

Added test for I/O to both JSON and pickle files

Also added test for add_to_parser

env option

specified as pathlib.Path objects, so they can be differentiated from input
values.

items (where possible). Result standard output renamed from "output" to
"stdout".

is used in conjunction with submit=True

double-barrelled filename support (but not HCP files :( )

This is now the new default behaviour when loading a new file

This change is not backwards compatible!

Image.save was resulting in a Nifti without a header.

There were some subtle bugs in the use of get_all, which should now be fixed. They were caused by having multiple optional variables and the result not being deterministic if these were iterated in different orders.

sure the MGHImage class preserves this.