Detect non-optional files that are missing at arbitrary depth in WDL task outputs

[adamnovak]

Right now when a WDL task produces output we check the top-level File type outputs to make sure they aren't null.

But if you write something like Array[Array[File]] out_lists = [["existent.txt"], ["existent2.txt", "nonexistent.txt"]] in a task output section, it won't catch that nonexistent.txt doesn't exist and it will make it out into the rest of the workflow.

See https://github.com/DataBiosphere/toil/pull/4994/files#diff-25bae5a8ed8562153b4341fdb0e2e59842b0659fd70209763746bbd3580fd6d5L2336-R2364 where we're adding a TODO about this but not actually fixing it.

┆Issue is synchronized with this Jira Story
┆Issue Number: TOIL-1610