improve File? task output processing

[mlin]

Replace a hack that caused problems (#614) with optional File/Directory outputs, related to when & how a nonexistent output path is changed to None.

[coveralls]

Pull Request Test Coverage Report for Build 3507053885

• 47 of 47 (100.0%) changed or added relevant lines in 2 files are covered.
• 2 unchanged lines in 2 files lost coverage.
• Overall coverage decreased (-0.02%) to 95.203%

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Files with Coverage Reduction	New Missed Lines	%
WDL/runtime/backend/docker_swarm.py	1	91.45%
WDL/runtime/task.py	1	95.79%

Totals
Change from base Build 3384709402:	-0.02%
Covered Lines:	7224
Relevant Lines:	7588

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💛 - Coveralls