Revert pulsar-side stdio redirection

It just happened to pass tests in
https://github.com/galaxyproject/galaxy/pull/15907 because the test
framework looks at the stdio and stderr attributes, which are merged
from tool_std{out,err} and job_std{out,err}.
It however fails the tests for detect_errors that specifically checks
tool_stdout and tool_stderr.

I think it is a good idea to let pulsar handle the stdio redirection,
but for this to work we'd have to ship parts of the command line to pulsar
for final assembly, and that seems like a bigger change.

lib/galaxy/jobs/command_factory.py

@@ -104,12 +104,12 @@ def build_command(
         else:
             commands_builder = CommandsBuilder(externalized_commands)
 
-    if not for_pulsar:
-        # Galaxy writes I/O files to outputs, Pulsar instruments own I/O redirection
-        io_directory = "../outputs"
-        commands_builder.capture_stdout_stderr(
-            f"{io_directory}/tool_stdout", f"{io_directory}/tool_stderr", stream_stdout_stderr=stream_stdout_stderr
-        )
+    # Galaxy writes I/O files to outputs, Pulsar uses metadata. metadata seems like
+    # it should be preferred - at least if the directory exists.
+    io_directory = "../metadata" if for_pulsar else "../outputs"
+    commands_builder.capture_stdout_stderr(
+        f"{io_directory}/tool_stdout", f"{io_directory}/tool_stderr", stream_stdout_stderr=stream_stdout_stderr
+    )
 
     # Don't need to create a separate tool working directory for Pulsar
     # jobs - that is handled by Pulsar.

test/integration/test_pulsar_embedded.py

@@ -36,5 +36,6 @@ test_tools = integration_util.integration_tool_runner(
         "tool_provided_metadata_9",
         "simple_constructs_y",
         "composite_output",
+        "detect_errors",
     ]
 )