Replaces deepcopy with a smarter copy implementation, which only copies the instance attributes.

This is a speedup of about 20x (and yes, the deepcopy was getting annoyingly slow in some of my code).

a file or sub-dir

present

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