Add "all-in-one" mechanism to janis translate

[illusional]

Currently, Janis prepares one tool per file, and (sub)workflows can reference an individual tool from a tools/ folder. This folder is automatically zipped and supplied to Cromwell through the dependencies input.

However, there will be occasions where it's more practical to generate an "all-in-one" workflow, which contains all the tool definitions, for example: uploading to the FISS API / Terra, sharing workflows etc.

This behaviour is already implemented (but untested for a while) in CWL:

janis-core/janis_core/translations/cwl.py

Lines 403 to 410 in 96718bc

	def translate_workflow_to_all_in_one(
	cls,
	wf,
	with_resource_overrides=False,
	is_nested_tool=False,
	allow_empty_container=False,
	container_override=None,
	) -> cwlgen.Workflow:

It's not yet defined for WDL [You can assert that no two tools will have the same task ID (although practically it occasionally happens)], though as long as you can keep tasks and workflows ordered (in the order they're seen), you shouldn't have too many issues.