nested directory getting lost between steps
hi! I'm unsuccessfully trying to run our CWL pipeline with toil. It looks like somehow intermediate date products get lost. The pipeline runs fine with the CWL reference runner. My logfile is filled with errors like:

```
2017-11-26 11:19:34,177 - toil.leader - WARNING - W/2/jobLmwkno    WorkflowException: [Errno 2] No such file or directory: u'/vault-tina/gijs/prefactor-cwl/runs/run_2017-11-26-11-18-25/results/out_tmpdir2RF79v/calibrated.MS/OBSERVATION/table.lock'
```

The intermediate folder seems to be empty. My guess this is probably related to our data products being nested directory structures and maybe in combination with docker.

To reproduce this issue you could:
* clone our repository https://github.com/EOSC-LOFAR/prefactor-cwl/tree/b5c080d10c659232b46dd9dcb2d9e4c19cc9febc
* run `make toil` in the checkout

Requirements:
 * git-lfs
 * Docker
 * virtualenv




diff --git a/src/toil/cwl/cwltoil.py b/src/toil/cwl/cwltoil.py
index 554747cd..cf01e686 100755
--- a/src/toil/cwl/cwltoil.py
+++ b/src/toil/cwl/cwltoil.py
@@ -455,12 +455,6 @@ class CWLJob(Job):
                                                 cwltool.stdfsaccess.StdFsAccess(outdir),
                                                 recursive=True))
 
-        def make_dir_literal(obj):
-            if "location" in obj and obj["location"].startswith("file:"):
-                obj["location"] = "_:" + str(uuid.uuid4())
-
-        adjustDirObjs(output, make_dir_literal)
-
         adjustFileObjs(output, functools.partial(uploadFile,
                                                  functools.partial(writeGlobalFileWrapper, fileStore),
                                                  index, existing))
['src/toil/cwl/cwltoil.py']