flagging a input Directory as writable still symlinks all files, not copy

hi!

When I define an input folder as writable it is still being symlinked. Example:

```
cwlVersion: v1.0
class: CommandLineTool

requirements:
- class: DockerRequirement
dockerFile: |
FROM kernsuite/base:1
RUN docker-apt-install aoflagger
dockerImageId: vermeerkat/aoflagger
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.ms)
entryname: flagged.ms
writable: true

baseCommand: "aoflagger"
arguments: ["flagged.ms"]

inputs:
ms: Directory

outputs:
ms:
type: Directory
outputBinding:
glob: flagged.ms
```

But if I then look inside the intermediate cached results, the recursive directory structure is created but all files are symlinked:

```
gijs@sherlock:~/vermeerkat-cwl/cache/085d5148d1d46592125b34efa141b372/flagged.ms (master)
λ ls -al
total 132
drwxr-xr-x 15 gijs gijs 4096 Jan 30 11:30 .
drwxrwxr-x 3 gijs gijs 4096 Jan 30 11:30 ..
drwxr-xr-x 2 gijs gijs 4096 Jan 30 11:30 ANTENNA
drwxr-xr-x 2 gijs gijs 4096 Jan 30 11:30 DATA_DESCRIPTION
drwxr-xr-x 2 gijs gijs 4096 Jan 30 11:30 FEED
drwxr-xr-x 2 gijs gijs 4096 Jan 30 11:30 STATE
lrwxrwxrwx 1 gijs gijs 84 Jan 30 11:30 table.dat -> /home/gijs/vermeerkat-cwl/cache/ca8d89e0b4b1c166a06924f8a8218b42/result.ms/table.dat
lrwxrwxrwx 1 gijs gijs 83 Jan 30 11:30 table.f0 -> /home/gijs/vermeerkat-cwl/cache/ca8d89e0b4b1c166a06924f8a8218b42/result.ms/table.f0
lrwxrwxrwx 1 gijs gijs 83 Jan 30 11:30 table.f1 -> /home/gijs/vermeerkat-cwl/cache/ca8d89e0b4b1c166a06924f8a8218b42/result.ms/table.f1
lrwxrwxrwx 1 gijs gijs 83 Jan 30 11:30 table.f2 -> /home/gijs/vermeerkat-cwl/cache/ca8d89e0b4b1c166a06924f8a8218b42/result.ms/table.f2
lrwxrwxrwx 1 gijs gijs 85 Jan 30 11:30 table.lock -> /home/gijs/vermeerkat-cwl/cache/ca8d89e0b4b1c166a06924f8a8218b42/result.ms/table.lock
```