fix(stages): modernise syntax

[MattWellie]

PR #18 2/3

A few syntax tweaks:

1. Removes the use of job/__init__.py to implicitly gather methods. The previous solution meant that from jobs import build_pyramid could refer to the module or the method, and was flagged by the linter as a namespace collision
2. Changes how the global/cached Batch instance (hail_batch.get_batch()) is accessed. Previously this was accessed in stages.py and passed as a method argument to every job. Here it is accessed where needed, and never passed as a method.
3. Return types added to all Stage methods
4. The output-path generating method self.expected_outputs is only called once per Stage, and the results are reused.
5. File paths are used as Path types, instead of being cast to Strings. Previously this was required as hail's read_input and write_output methods only tolerated Strings; changed since Hail 0.2.133.
6. Many ignored linting rules are reactivated, including import sorting
7. Many redundant lines are removed, e.g.

command = "..."
job.command(command)

is replaced with: job.command("...")