Use sentinel value to deal with optional coerced files (#4994)

* Don't immediately virtualize
(may want to remove monkeypatching entirely)

* Try sentinel implementation

* add abstracted function and remove duplicated execution_dir in standard
library for task outputs

* fix typo and satisfy mypy with getattr

* Fix instance type checks as we were checking WDL types to WDL values

* Add documentation, fix variable names, remove unused

* Missing type annotation

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>