fix output discovery

1. `primary_output_assigned` needs to be reset for each output

   lets say there are two outputs: `datasets` (a normal dataset)
   and `discovered` (discovered datasets). if `datasets` is
   processed after `discovered` then `primary_output_assigned`
   is still true from the first loop (where `discovered` was precessed).
   this leads to overwriting of info (e.g. name) of the `dataset` output
   (in the `if primary_output_assigned` branch at the end of the outer
   loop).

2. assign_primary_output must be obeyed for all outputs (not just the
   first).

   sticking to the above example, `assign_primary_output` would
   work only if `dataset` is processed after `discovered`

lib/galaxy/job_execution/output_collect.py

@@ -474,11 +474,11 @@ def collect_primary_datasets(job_context: Union[JobContext, SessionlessJobContex
 
     # Loop through output file names, looking for generated primary
     # datasets in form specified by discover dataset patterns or in tool provided metadata.
-    primary_output_assigned = False
     new_outdata_name = None
     primary_datasets: Dict[str, Dict[str, Union[HistoryDatasetAssociation, LibraryDatasetDatasetAssociation]]] = {}
     storage_callbacks: List[Callable] = []
-    for output_index, (name, outdata) in enumerate(output.items()):
+    for name, outdata in output.items():
+        primary_output_assigned = False
         dataset_collectors = [DEFAULT_DATASET_COLLECTOR]
         output_def = job_context.output_def(name)
         if output_def is not None:
@@ -504,7 +504,7 @@ def collect_primary_datasets(job_context: Union[JobContext, SessionlessJobContex
             dbkey = fields_match.dbkey
             if dbkey == INPUT_DBKEY_TOKEN:
                 dbkey = job_context.input_dbkey
-            if filename_index == 0 and extra_file_collector.assign_primary_output and output_index == 0:
+            if filename_index == 0 and extra_file_collector.assign_primary_output:
                 new_outdata_name = fields_match.name or f"{outdata.name} ({designation})"
                 outdata.change_datatype(ext)
                 outdata.dbkey = dbkey