"File staging conflict" error is suppressed when using a container; files get overwritten

When you try to stage input files with an InitialWorkDirRequirement, and the files have the same name, they normally trigger an error that halts the workflow. However, if you are using a Singularity container, the error message does not arise and the files get silently overwritten.

Here is code reproducing the error;

`make_file.cwl`

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

cwlVersion: v1.0
class: CommandLineTool
baseCommand: [ "bash", "run.sh" ]

stdout: output.txt

requirements:
InitialWorkDirRequirement:
listing:
- entryname: run.sh
entry: |-
echo "$1"

inputs:
sampleId:
type: string
inputBinding:
position: 1

outputs:
output_file:
type: stdout
```

`cat.cwl`

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

cwlVersion: v1.0
class: CommandLineTool
baseCommand: [ "bash", "run.sh" ]

requirements:
# DockerRequirement: # <- this is the part that causes the error
# dockerPull: ubuntu:latest
InitialWorkDirRequirement:
listing:
- entryname: some_dir # <- put all the input files into a dir
writable: true
entry: "$({class: 'Directory', listing: inputs.input_files})"
- entryname: run.sh
entry: |-
for i in \$(find some_dir -type f); do cat \$i ; done

stdout: output.txt

inputs:
input_files:
type: File[]

outputs:
output_file:
type: stdout

```

`workflow.cwl`

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

cwlVersion: v1.0
class: Workflow
requirements:
MultipleInputFeatureRequirement: {}
ScatterFeatureRequirement: {}
StepInputExpressionRequirement: {}
InlineJavascriptRequirement: {}
SubworkflowFeatureRequirement: {}

inputs:
samples:
type:
type: array
items:
type: record
fields:
sampleId: string

steps:
make_file:
run: make_file.cwl
scatter: sample
in:
sample: samples
sampleId:
valueFrom: ${ return inputs.sample['sampleId']; }
out:
[ output_file ]

gather_files:
run: cat.cwl
in:
input_files: make_file/output_file
out:
[ output_file ]

outputs:
output_file:
type: File
outputSource: gather_files/output_file
```

`input.json`

```
{"samples":[ {"sampleId":"Sample1"}, {"sampleId":"Sample2"} ]}
```

Running the command without a container gives this error message

```
$ cwltool --outdir output --tmpdir-prefix tmp --tmp-outdir-prefix tmp --leave-tmpdir workflow.cwl input.json
INFO /home/conda/bin/cwltool 3.0.20201203173111
INFO Resolved 'workflow.cwl' to 'file:///home/_test_cwl_initialDir/workflow.cwl'
INFO [workflow ] start
INFO [workflow ] starting step make_file
INFO [step make_file] start
INFO [job make_file] /home/_test_cwl_initialDir/tmp5h392ved$ bash \
run.sh \
Sample1 > /home/_test_cwl_initialDir/tmp5h392ved/output.txt
INFO [job make_file] completed success
INFO [step make_file] start
INFO [job make_file_2] /home/_test_cwl_initialDir/tmpg5gfplqz$ bash \
run.sh \
Sample2 > /home/_test_cwl_initialDir/tmpg5gfplqz/output.txt
INFO [job make_file_2] completed success
INFO [step make_file] completed success
INFO [workflow ] starting step gather_files
INFO [step gather_files] start
ERROR Workflow error, try again with --debug for more information:
File staging conflict, trying to stage both /home/_test_cwl_initialDir/tmp5h392ved/output.txt and /home/_test_cwl_initialDir/tmpg5gfplqz/output.txt to the same target /home/_test_cwl_initialDir/tmpmyxk4qg7/some_dir/output.txt
```

However, if we modify `cat.cwl` to un-comment these lines;

```
DockerRequirement:
dockerPull: ubuntu:latest
```

And re-run with Singularity, no error is shown;

```
$ cwltool --singularity --outdir output --tmpdir-prefix tmp --tmp-outdir-prefix tmp --leave-tmpdir workflow.cwl input.json
INFO /home/conda/bin/cwltool 3.0.20201203173111
INFO Resolved 'workflow.cwl' to 'file:///home/_test_cwl_initialDir/workflow.cwl'
INFO [workflow ] start
INFO [workflow ] starting step make_file
INFO [step make_file] start
INFO [job make_file] /home/_test_cwl_initialDir/tmp53kze362$ bash \
run.sh \
Sample1 > /home/_test_cwl_initialDir/tmp53kze362/output.txt
INFO [job make_file] completed success
INFO [step make_file] start
INFO [job make_file_2] /home/_test_cwl_initialDir/tmp95ehrjx1$ bash \
run.sh \
Sample2 > /home/_test_cwl_initialDir/tmp95ehrjx1/output.txt
INFO [job make_file_2] completed success
INFO [step make_file] completed success
INFO [workflow ] starting step gather_files
INFO [step gather_files] start
INFO Using local copy of Singularity image found in /home/_test_cwl_initialDir
INFO [job gather_files] /home/_test_cwl_initialDir/tmpqm_u_50b$ singularity \
--quiet \
exec \
--contain \
--ipc \
--pid \
--home \
/home/_test_cwl_initialDir/tmpqm_u_50b:/jPTSKv \
--bind \
/home/_test_cwl_initialDir/tmpzqg0emi1:/tmp:rw \
--pwd \
/jPTSKv \
/home/_test_cwl_initialDir/ubuntu:latest.sif \
bash \
run.sh > /home/_test_cwl_initialDir/tmpqm_u_50b/output.txt
INFO [job gather_files] completed success
INFO [step gather_files] completed success
INFO [workflow ] completed success
{
"output_file": {
"location": "file:///home/_test_cwl_initialDir/output/output.txt",
"basename": "output.txt",
"class": "File",
"checksum": "sha1$24c5362ecd1bfafba85f185f28b12c121d03ee12",
"size": 8,
"path": "/home/_test_cwl_initialDir/output/output.txt"
}
}
INFO Final process status is success
```

The output of the workflow is;

```
$ cat output/output.txt
Sample2
```

`Sample1` is not present because the file that contained that string, `/home/_test_cwl_initialDir/tmp53kze362/output.txt`, got overwritten;

```
$ tree tmpqm_u_50b/
tmpqm_u_50b/
├── run.sh
└── some_dir
└── output.txt

$ cat tmpqm_u_50b/some_dir/output.txt
Sample2
```

It seems like this is triggered by the inclusion of the `DockerRequirement` in the CWL, since running the CWL without the `DockerRequirement` but with `--singularity` enable still triggers the error as expected.

So I guess the best solution would be for `cwltool` to trigger the same error message in cases like this.

## Your Environment
* cwltool version: 3.0.20201203173111