Using DNAx workflow inputs and outputs

• Uplift the code to use DNAnexus workflow inputs and outputs.
  Running a workflow now has slighly easier command line syntax.
  For example, if workflow foo takes an integer
  argument N, then running it through the CLI is done like
  this:

dx run foo -iN=19                                                                                                      

• Revamp the conversions between dx:file and wdl:file. This allows
  specifying dx files in defaults.

• Initial support for non-empty WDL array types, for example Array[String]+.

• Improved handling of optional values

• An experimental new syntax for specifying inputs where the workflow
  is underspecified. WDL allows leaving required call inputs unassigned, and
  specifying them from the input file. For example, workflow math
  calls task add, but does not specify argument b. It can then
  be specified from the input file as follows: { "math.add.b" : 3}.

task add {
    Int a
    Int b
    output {
        Int result = a + b
    }
}

workflow math {
    call add { input: a = 3 }                                                                                          
    output {                                                                                                           
       add.result                                                                                                      
    }                                                                                                                  
}

The dx:workflow that is compiled from math can set this variable from
the command line as follows:

dx run math -iadd___b=5                                                                                                

This command line syntax may change in the future.