PTFM-12607: adding bash helper variables

Summary:
1. Refactoring of code, so as to achieve sharing, between local and remote execution.
2. Adding several bash variables available to the application: filenames, prefixes, and paths.
3. Reducing the number of file uploads, to reduce runtime
4. Marking tests correctly, so as not to run jobs

Test Plan: application tests

Reviewers: klai

Reviewed By: klai

Differential Revision: https://phabricator.dnanexus.com/D140