CLI File Provisioning doesn't handle all input types with files for WDL

[coverbeck]

Describe the bug
When provisioning for a WDL workflow, the CLI correctly handles input parameters of type File and Array[File]. There are other input types that can have files that need to be provisioned -- the bug was found for an input of type Array[Array[File]]. Speculatively, it might happen also happen with Pair, Map and/or Struct types, although we're not clear how you'd represent those in the parameter JSON.

To Reproduce
Steps to reproduce the behavior:

1. If you haven't already, configure the CLI to use Google Cloud Storage.
2. Create and save this JSON as test.json

{
  "myco.paired_decontaminated_fastq_sets": [
    [
      "gs://ucsc-pathogen-genomics-public/tb/fq/gz/SAMEA3512769_ERR987753_1.fastq.gz",
      "gs://ucsc-pathogen-genomics-public/tb/fq/gz/SAMEA3512769_ERR987753_2.fastq.gz"
    ]
  ]
}

1. Run dockstore workflow launch --entry github.com/aofarrel/myco/myco_simple:6.0.0 --json test.json
2. Workflow should run, but it fails, and you won't see any messages that it copied the gs files.

Expected behavior
The workflow should get provisioned.

Additional context

See this line, where the workflow input is defined as an Array[Array[File]].

Here's the code where we only check for File and Array[File].

See #5680, where this bug was discovered.

Version

dockstore -v
Current version : 1.14.0
You have the most recent stable release.
If you wish to upgrade to the latest unstable version, please use the following command:
   dockstore --upgrade-unstable
Dockstore version 1.14.0
You are running the latest stable version.

┆Issue is synchronized with this Jira Story
┆Fix Versions: Dockstore 2.X
┆Issue Number: DOCK-2500
┆Sprint: Backlog
┆Issue Type: Story