inconsistent behavior: passing file paths via command line arguments vs input job documents

``` yaml
#!/usr/bin/env cwl-runner

cwlVersion: cwl:draft-3
class: CommandLineTool

baseCommand: wc

inputs:
- id: inputfile
type: File
inputBinding:
position: 1

outputs:
- id: outputfile
type: File
outputBinding:
glob: $((inputs.inputfile.path + '.wc').replace(runtime.outdir + '/', ''))

stdout: $(inputs.inputfile.path + '.wc')

requirements:
- class: InlineJavascriptRequirement
```

``` bash
(env) mcrusoe@mrcdev:~/t$ cwl-runner wc3.cwl --inputfile input.txt
/home/mcrusoe/t/env/bin/cwl-runner 1.0.20160507101510
[job wc3.cwl] /home/mcrusoe/t$ wc /home/mcrusoe/t/input.txt > /home/mcrusoe/t/input.txt.wc
Final process status is success
{
"outputfile": {
"size": 32,
"path": "/home/mcrusoe/t/input.txt.wc",
"checksum": "sha1$843dfe5163bcb9cc33b20d0142a10db395a71ccd",
"class": "File"
}
}
```

vs using an input document

```
inputfile:
class: File
path: input.txt
```

``` bash
(env) mcrusoe@mrcdev:~/t$ rm input.txt.wc
(env) mcrusoe@mrcdev:~/t$ cwl-runner wc3.cwl wc2-job1.yml
/home/mcrusoe/t/env/bin/cwl-runner 1.0.20160507101510
[job wc3.cwl] /home/mcrusoe/t$ wc /home/mcrusoe/t/input.txt > /home/mcrusoe/t/file:///home/mcrusoe/t/input.txt.wc
Error while running job: Error collecting output for parameter 'outputfile': Did not find output file with glob pattern: '[u'input.txt.wc']'
[job wc3.cwl] completed permanentFail
Final process status is permanentFail
Workflow error, try again with --debug for more information:
Process status is ['permanentFail']
```