Allow setting schema_dir at runtime, overriding YAML contents

[baltzell]

A new option --schemaDir can copy in the YAML file locally and modify it in the job, replacing schema_dir (or adding it if it doesn't exist) with the CLI option.

The YAML is the one thing that can be altered by users after workflow generation, if they add the write bit or "rm -f" and remake it, both of which are bad.

Another option is to copy it to a temporary location, but I'm not sure that overhead is worth it and can lead to other complications.

[raffaelladevita]

I like the idea of the new --shemaDir option because often chefs use multiple yamls that differ only for the schema directory to produce different output types.

I agree that changing the yaml after the workflow is generated should be discouraged and the option of copying the yaml seems indeed a potential source of (other) problems.

[baltzell]

We could also read the YAML in the job from the README.json that is generated at submit time.