WDL 1.1 support bugs

[vsmalladi]

Using wdl-test and SPEC.md I found a number of errors that can be grouped into the following issues:

• [ ] Object support #694 and #684

• test_object.wdl

• read_object_task.wdl

• read_objects_task.wdl

• write_object_task.wdl

• write_objects_task.wdl

• [x] Structs

  • test_struct.wdl #728
  • map_to_struct.wdl #712

• [x] Return Codes #729

  • single_return_code_task.wdl
  • all_return_codes_task.wdl

• [x] POSIX regex standard #709

• test_1.1/test_sub.wdl

• [x] Boolean evaluation #701

  • read_bool_task.wdl

• [ ] JSON Serialization of integers #702

  • write_json_fail.wdl

• [x] Transpose array no equivalent to explicit #699

  • test_transpose.wdl

• [x] Map to struct coercion #712

  • test_as_map.wdl

• [x] Map has error with nested File types #700

  • test_collect_by_key.wdl

• [ ] Let task output files outside its working directory #214

  • relative_and_absolute_task.wdl

• [ ] Optional file for select_all not consistent #696

  • file_sizes_task.wdl

[mlin]

@vsmalladi Thanks a lot for compiling this, really helpful!