Unable to omit 'Unrecognized extension field' warnings for fields in RDF schema

Hi,
The attachment contains test files to reproduce the issue (CWL and the xml schema file) - [cwl-schemas.tar.gz](https://github.com/common-workflow-language/common-workflow-language/files/1660407/cwl-schemas.tar.gz)

When running the tool with cwltool version 1.0.20180116213856 an 'Unrecognized extension field' warning is printed out. While running with an older version (1.0.20170413194156) there was no warning.
`cwltool schemas-tool1.cwl -- --input foobar`

## Expected Behavior
After including $schemas in the CWL, cwltool should not print out a warning.

## Actual Behavior
After including $schemas in the CWL, cwltool version 1.0.20180116213856 prints out a warning.

## Workflow Code
```
class: CommandLineTool
cwlVersion: v1.0
id: schema
baseCommand:
- echo
inputs:
- id: input
type: string?
inputBinding:
position: 0
outputs:
- id: output
type: File?
outputBinding:
glob: stdout.txt
label: schemas-tool1
requirements:
- class: DockerRequirement
dockerPull: 'ubuntu:16.04'
stdout: stdout.txt
$namespaces:
sbg: 'http://sbgenomics.com/schema#'
$schemas:
- sbg-schema.xml
'sbg:appVersion':
- v1.0
```

## Full Traceback
```pytb
schemas-tool1.cwl:1:1: unrecognized extension field `http://sbgenomics.com/schema#appVersion`. Did you include a $schemas section?
```

## Your Environment
* cwltool version: 1.0.20180116213856
Check using ``cwltool --version``