restore previous logic

Yes, a bit odd that `class: Directory` objects in `listing` had a `dirname`,
but we are temporarily using that (and fixing them) for setting the outdir when
updating the Pathmapper. Then the `dirname` fields are removed
immediately after.

Author: mr-c

cwltool/command_line_tool.py

@@ -757,17 +757,17 @@ def _initialworkdir(self, j: JobBase | None, builder: Builder) -> None:
                 if "basename" in entry:
                     basename = cast(str, entry["basename"])
                     entry["basename"] = os.path.basename(basename)
+                    dirname = os.path.join(builder.outdir, os.path.dirname(basename))
+                    entry["dirname"] = dirname
                     if is_file(entry):
-                        dirname = os.path.join(builder.outdir, os.path.dirname(basename))
-                        entry["dirname"] = dirname
                         if "secondaryFiles" in entry:
                             for sec_file in cast(
                                 MutableSequence[CWLObjectType], entry["secondaryFiles"]
                             ):
                                 sec_file["dirname"] = dirname
                 normalizeFilesDirs(entry)
                 self.updatePathmap(
-                    (entry.get("dirname") if is_file(entry) else None) or builder.outdir,
+                    cast(Optional[str], entry.get("dirname")) or builder.outdir,
                     cast(PathMapper, builder.pathmapper),
                     entry,
                 )