InitialWorkDir contents must be read-only by default

[anton-khodak]

Related conformance test: common-workflow-language/common-workflow-language#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.