fix: wdl run should join input paths correctly.

[peterhuene]

This PR fixes the wdl run command to properly join input paths relative to the inputs file.

The code to make the path of the inputs file absolute was incorrectly done, resulting in the later join_paths call to effectively be a no-op when the inputs file path on the command line was relative to CWD (e.g. ./foo.json).

As a result, task execution would fail when using the path as the path would then be treated as relative to the task's working directory as it was not made absolute.

The fix is to simply return the absolute path correctly from parse_inputs.

Fixes #301.

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[a-frantz]

Changes look good! But can we add some comments to the body of parse_inputs() to clarify what's happening? It's a bit messy and hard to follow IMO.

[peterhuene]

Done.

[adthrasher]

Appreciate the extra comments!