extraneous warning: optional input connected to step with required input that has a default value

dynresreq-workflow-stepdefault.cwl:
```
#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.0

inputs:
special_file: File?
outputs:
cores:
type: File
outputSource: report/output

steps:
count:
in:
special_file:
source: special_file
default:
class: File
location: special_file
out: [output]
run: dynresreq.cwl

report:
in:
file1: count/output
out: [output]
run: cat-tool.cwl
```
(the remaining files are from the CWL v1.0 repo)

```
/home/mcrusoe/src/toil/venv/bin/cwltool 1.0.20180508202931
Resolved 'v1.0/dynresreq-workflow.cwl' to 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/dynresreq-workflow.cwl'
Workflow checker warning:
v1.0/dynresreq-workflow.cwl:6:3: Source 'special_file' of type ["null", "File"] may be incompatible
v1.0/dynresreq-workflow.cwl:15:7: with sink 'special_file' of type "File"
```

Start by running cwltool against dynresreq-workflow-stepdefault.cwl and comparing the reported workflow checker warning with the optional source and default shown in the issue. Trace the checker entry point that emits this warning; done means this valid workflow no longer produces the extraneous incompatibility warning while genuine type incompatibilities remain reported.

Written by the indexing model from the issue text.