fixing PTFM-12607

1. Refactoring of code, so as to acheive 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...

Summary:
...reduce runtime
4. Marking tests correctly, so as not to run jobs
5. Changing _filename to _name

Fixing a problem with PTFM-12607-bash-helper-variables

Test Plan: application tests

Reviewers: klai

Differential Revision: https://phabricator.dnanexus.com/D140
Merge branch 'bash-helpers-fix' of github.com:dnanexus/dx-toolkit into bash-helpers-fix