Saving a command file needs both `requires_dir` and `save_files` keys

[gcapes]

The documentation says that you need a save_files key, which makes sense, but that only works if you also have a requires_dir key too. Without either key, or with just the save_files key, the files are saved to artifacts/submissions/0/tmp. Only when using both keys, are the named files saved under artifacts/tasks.

The docs kinda suggest that save_files saves files, but there's nothing to explain that it only works if you use requires_dir. requires_dir doesn't have any explanation.

In the first instance, the docs should reflect how things actually work, but longer term, it would make more sense if save_files did what the name suggests without needing an undocumented helper key (requires_dir).

[gcapes]

@aplowman
An example for reproducing this behaviour is in the docs: https://docs.matflow.io/stable/user/getting_started/advanced_workflow_concepts.html

template_components:
  task_schemas:
  - objective: process_data
    inputs:
    - parameter: input_data
    outputs:
    - parameter: parsed_output
    actions:
    - input_file_generators:
      - input_file: my_input_file
        from_inputs:
        - input_data
        script: <<script:/full/path/to/generate_input_file.py>>
      environments:
      - scope:
          type: any
        environment: python_env
      script_exe: python_script
      script: <<script:/full/path/to/process_input_file.py>>
      save_files:
      - processed_file
      output_file_parsers:
        parsed_output:
          from_files:
          - my_input_file
          - processed_file
          script: <<script:/full/path/to/parse_output.py>>
          save_files:
            - parsed_output

  - objective: process_data_without_input_file_generator
    inputs:
    - parameter: input_data
    - parameter: path
    actions:
    - script: <<script:/full/path/to/generate_input_file.py>>
      script_data_in: direct
      script_exe: python_script
      save_files:
      - my_input_file
      environments:
      - scope:
          type: any
        environment: python_env
      requires_dir: true
    - script: <<script:/full/path/to/process_input_file.py>>
      script_exe: python_script
      environments:
      - scope:
          type: any
        environment: python_env
      save_files:
      - processed_file
      requires_dir: true

  command_files:
  - label: my_input_file
    name:
      name: input_file.json
  - label: processed_file
    name:
      name: processed_file.json
  - label: parsed_output
    name:
      name: parsed_output.json


tasks:
- schema: process_data
  inputs:
    input_data: [1, 2, 3, 4]
- schema: process_data_without_input_file_generator
  inputs:
    input_data: [1, 2, 3, 4]
    path: input_file.json

The python scripts required for this are on the previous page: https://docs.matflow.io/stable/user/getting_started/custom_task_schemas_and_workflows.html#example-workflow

The above workflow runs just fine, but if you remove requires_dir: true from either action within the process_data_without_input_file_generator task, the workflow fails as described in the initial comment above.