Fix many issues with examples

[jdidion]

Closes #653.
Closes #654.
Closes #661.
Closes #662.
Closes #663.
Closes #664.
Closes #665.
Closes #666.
Closes #667.
Closes #668.

Checklist

• Pull request details were added to CHANGELOG.md

[jdidion]

@stxue1 @adamnovak would also appreciate your reviews

[adamnovak]

This looks like everything should work.

[stxue1]

The unit test test_hints wc command is malformed:

wdl/SPEC.md

Line 4584 in 20ff54d

wc -l ~{foo}

And should be:

  wc -l < ~{foo}

The expected output should change from 3 to 2 as well:

wdl/SPEC.md

Line 4619 in 20ff54d

"test_hints.num_lines": 3

{
  "test_hints.num_lines": 2
}

[stxue1]

input_hint is missing an output:

wdl/SPEC.md

Lines 4703 to 4705 in 20ff54d

	```json
	{}
	```

I'm not too certain what the expected output should be. MiniWDL currently returns

{
    "input_hint.experience": []
}

[claymcleod]

input_hint is missing an output:

wdl/SPEC.md

Lines 4703 to 4705 in 20ff54d

	```json
	{}
	```

I'm not too certain what the expected output should be. MiniWDL currently returns

{
    "input_hint.experience": []
}

This has also been resolved.

Based on this, I think the PR is good to go, and I'm going to merge it. This PR has sat for a second, so I did the best I could with making sure nothing was missed, but feel free to file another issue if anything wasn't pulled in correctly.