[hailtop.batch] Restructure and use better types for resources

[danking]

This was spawned by https://github.com/hail-is/hail/pull/14310 which slipped into 0.2.126 because we do not have types on some of our inner functions. In my attempt to type everything, I discovered a really perplexing function _add_resource_to_set.

I was able to give it a type but it was really complicated, involved @overload, and did not seem to help me reason about that function. I presumed the root cause was that the Resource class had an insufficient interface.

Here is how I understand what that function was trying to achieve: We need to track the set of resources that are produced by, produced-by-and-later-consumed, and consumed by a job:

1. "Produced by" corresponds to Job._valid.
2. "Produced-by-and-later-consumed" corresponds to Job._internal_outputs and Job._external_outputs.
3. "Consumed by" corresponds to Job._inputs.

There is also Job._mentioned which I do not fully understand but which does not use _add_resource_to_set.

There is an important distinction between the latter two and the first kind of resource set. The latter two must be what I am now calling SingleResources. These are actual single files that need to be uploaded or downloaded. In contrast the "produced by" set (and, I think Job._mentioned) might include ResourceGroups which are composite: one or more SingleResources that must be transmitted as a group.

For example, a VCF file and its TBI index file must always be transmitted as a group, even if a job only references one of those two files. That's the essential functionality of a ResourceGroup.

I introduced three operations to Resource which I think make this system simpler:

1. get_resource_group: if a Resource is a group or a member thereof, return it.

2. component_resources: if a Resource is composite, return the components, otherwise just return the resource itself.

3. bonded_resources: the minimum set of resources that must be transmitted if this resource is transmitted. In particular, a member of a resource group returns itself and the other resources in the group. A resource group just returns its components.

We can now add a type annotation which requires (2) and (3) to be sets of SingleResource. In particular, (2) and (3) are concrete files that can be copied as opposed to groups thereof.