Bad level of secondaryFiles in outputs doesn't throw an error

## Expected Behavior

When an `outputBinding` (possibly other areas too) has `secondaryFiles` defined at the wrong level an error should be thrown.

## Actual Behavior

When indented too far secondaryFiles is not interpreted and no validation errors are raised

```
outputs:
out_cram:
type: File
outputBinding:
glob: $(inputs.sample).cram
secondaryFiles:
- .crai
```

cwltool happily processes but the `.crai` file is not captured.

## Full Traceback

no error is raised bad config results in stdout of:

```
{
"out_bam": {
"checksum": "sha1$e9e4c479937e797baf0f570b71bff0fd6de71138",
"basename": "test.bam",
"location": "file:///home/ubuntu/datastore/launcher-4ba554fc-47d6-472d-b1c6-26955e8f600c/outputs/test.bam",
"path": "/home/ubuntu/datastore/launcher-4ba554fc-47d6-472d-b1c6-26955e8f600c/outputs/test.bam",
"class": "File",
"size": 6600410
}
}
```

## Your Environment

```
/usr/local/bin/cwltool 1.0.20170828135420
```