Missing input in allow_nested.wdl unit test

[stxue1]

For the allow_nested.wdl unit test, these lines call a task and omits a required input:

wdl/SPEC.md

Lines 5655 to 5658 in 9c0b9cf

	call lib.repeat as repeat2 {
	input:
	opt_string = msg2
	}

This line clarifies that with allowNestedInputs directive, this input can be supplied elsewhere:

repeat2.i may be set by the caller of the workflow, e.g., by including "allow_nested.repeat2.i": 2, in the input JSON.

However, for the unit test, I don't see this input being passed through:

wdl/SPEC.md

Lines 5677 to 5685 in 9c0b9cf

	```json
	{
	"allow_nested.int_val": 3,
	"allow_nested.msg1": "hello",
	"allow_nested.msg2": "goodbye",
	"allow_nested.my_ints": [1, 2, 3],
	"allow_nested.ref_file": "hello.txt"
	}
	```

Instead, there is an expected output that wants the same variable:

wdl/SPEC.md

Line 5693 in 9c0b9cf

"allow_nested.repeat2.i": 2,

As I don't see where repeat2.i is defined in the workflow/input JSON, it looks like that line in the example output JSON should be moved to the example input JSON; the spec also doesn't say (at least to my knowledge) that the execution engine should output certain task inputs from nested calls when there is a output section.

[stxue1]

A similar issue is in the outputs_task.wdl, there's an input in the JSON:

wdl/SPEC.md

Line 3694 in 9c0b9cf

"outputs.write_outstr": false

But it doesn't exist in the inputs:

wdl/SPEC.md

Lines 3671 to 3673 in 9c0b9cf

	input {
	Int t
	}