Fixes job working directory resolution

The previous implementation relied on a configuration fallback that incorrectly mapped the global object-store base directory to individual jobs. Reading directly from the destination parameters prevents this unintended override and ensures resubmitted jobs correctly resolve their custom working directories.

Author: davelopez

lib/galaxy/jobs/__init__.py

@@ -1875,7 +1875,7 @@ def _set_working_directory(self, job: Job):
         ``clear_working_directory``) must flush/commit themselves. The enqueue
         path is covered by the ``commit()`` in ``enqueue()``.
         """
-        working_directory = self.get_destination_configuration("job_working_directory", None)
+        working_directory = self.job_destination.params.get("job_working_directory", None)
         if isinstance(working_directory, str):
             validate_working_directory_path(working_directory)
             job.working_directory = working_directory

lib/galaxy/jobs/runners/state_handlers/resubmit.py

@@ -113,10 +113,9 @@ def _handle_resubmit_definitions(
         # Persist the new destination before clearing the working directory.
         # set_job_destination() assigns job.destination_params = new_destination.params
         # and flushes, so when clear_working_directory() → _setup_working_directory()
-        # → _set_working_directory() calls get_destination_configuration(), the model's
-        # get_destination_configuration (model/__init__.py) reads job.destination_params
-        # first — which now holds the *new* params, not the stale values from the prior
-        # attempt. This is what makes a resubmitted job resolve its new JWD correctly.
+        # → _set_working_directory() reads self.job_destination.params, which now
+        # holds the *new* params, not the stale values from the prior attempt.
+        # This is what makes a resubmitted job resolve its new JWD correctly.
         job_state.job_wrapper.set_job_destination(new_destination)
         # Reset job state. clear_working_directory() flushes the session after
         # _setup_working_directory() → _set_working_directory() mutates the