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

• [x] Pull request details were added to CHANGELOG.md

[jdidion]

@stxue1 @adamnovak would also appreciate your reviews

[stxue1]

The unit test test_hints wc command is malformed: https://github.com/openwdl/wdl/blob/20ff54d261e44e903d94149eb1f5c4dd141d26ea/SPEC.md?plain=1#L4584

And should be:

  wc -l < ~{foo}

The expected output should change from 3 to 2 as well: https://github.com/openwdl/wdl/blob/20ff54d261e44e903d94149eb1f5c4dd141d26ea/SPEC.md?plain=1#L4619

{
  "test_hints.num_lines": 2
}

[stxue1]

input_hint is missing an output: https://github.com/openwdl/wdl/blob/20ff54d261e44e903d94149eb1f5c4dd141d26ea/SPEC.md?plain=1#L4703-L4705

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

{
    "input_hint.experience": []
}

[claymcleod]

input_hint is missing an output:

https://github.com/openwdl/wdl/blob/20ff54d261e44e903d94149eb1f5c4dd141d26ea/SPEC.md?plain=1#L4703-L4705

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.