InitialWorkDir contents must be read-only by default

Related conformance test: https://github.com/common-workflow-language/common-workflow-language/issues/591

Implementation hints:

- before staging, record the permission bits of the files
- try to change the permission bits of the files recursively to be read-only for all users, the file's group, the file's user

(this is the equivalent of:
```
chmod -R a-r
```
and if that fails
```
chmod -R o-r
chmod -R g-r
chmod -R u-r
```
)
- after the step execution, write back the permission bits.