diff --git a/lib/galaxy/jobs/command_factory.py b/lib/galaxy/jobs/command_factory.py
index bef8a34e14e..f24aa3596ba 100644
--- a/lib/galaxy/jobs/command_factory.py
+++ b/lib/galaxy/jobs/command_factory.py
@@ -82,7 +82,10 @@ def build_command(
 
     __handle_task_splitting(commands_builder, job_wrapper)
 
+    externalized = False
+    for_pulsar = "pulsar_version" in remote_command_params
     if (container and modify_command_for_container) or job_wrapper.commands_in_new_shell:
+        externalized = True
         if container and modify_command_for_container:
             # Many Docker containers do not have /bin/bash.
             external_command_shell = container.shell
@@ -103,10 +106,13 @@ def build_command(
         else:
             commands_builder = CommandsBuilder(externalized_commands)
 
-    for_pulsar = "script_directory" in remote_command_params
-    if not for_pulsar:
+    wrap_stdio = externalized or not for_pulsar
+    if wrap_stdio:
+        # 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(
-            "../outputs/tool_stdout", "../outputs/tool_stderr", stream_stdout_stderr=stream_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
@@ -201,7 +207,7 @@ def __externalize_commands(
     #   doesn't need to mount the job directory (rw) and then eliminate this hack
     #   (or restrict to older Pulsar versions).
     #   https://github.com/galaxyproject/galaxy/pull/8449
-    for_pulsar = "script_directory" in remote_command_params
+    for_pulsar = "pulsar_version" in remote_command_params
     if for_pulsar:
         commands = f"{shell} {join(remote_command_params['script_directory'], script_name)}"
     log.info(f"Built script [{local_container_script}] for tool command [{tool_commands}]")
@@ -260,6 +266,7 @@ def __handle_metadata(
     config_file = metadata_kwds.get("config_file", None)
     datatypes_config = metadata_kwds.get("datatypes_config", None)
     compute_tmp_dir = metadata_kwds.get("compute_tmp_dir", None)
+    version_path = job_wrapper.job_io.version_path
     resolve_metadata_dependencies = job_wrapper.commands_in_new_shell
     metadata_command = (
         job_wrapper.setup_external_metadata(
@@ -272,6 +279,7 @@ def __handle_metadata(
             config_file=config_file,
             datatypes_config=datatypes_config,
             compute_tmp_dir=compute_tmp_dir,
+            compute_version_path=version_path,
             resolve_metadata_dependencies=resolve_metadata_dependencies,
             use_bin=job_wrapper.use_metadata_binary,
             kwds={"overwrite": False},
diff --git a/lib/galaxy/jobs/runners/pulsar.py b/lib/galaxy/jobs/runners/pulsar.py
index 0dcc371bb8c..1ddb01d3690 100644
--- a/lib/galaxy/jobs/runners/pulsar.py
+++ b/lib/galaxy/jobs/runners/pulsar.py
@@ -485,15 +485,17 @@ class PulsarJobRunner(AsynchronousJobRunner):
             remote_working_directory = remote_job_config["working_directory"]
             remote_job_directory = os.path.abspath(os.path.join(remote_working_directory, os.path.pardir))
             remote_tool_directory = os.path.abspath(os.path.join(remote_job_directory, "tool_files"))
+            pulsar_version = PulsarJobRunner.pulsar_version(remote_job_config)
             remote_command_params = dict(
                 working_directory=remote_job_config["metadata_directory"],
                 script_directory=remote_job_directory,
                 metadata_kwds=metadata_kwds,
                 dependency_resolution=dependency_resolution,
+                pulsar_version=pulsar_version,
             )
-            # TODO: Following directories work for Pulsar, always worked for Pulsar - but should be
-            # calculated at some other level.
-            job_wrapper.disable_commands_in_new_shell()
+            rewrite_paths = not PulsarJobRunner.__rewrite_parameters(client)
+            if pulsar_version < packaging.version.parse("0.14.999") and rewrite_paths:
+                job_wrapper.disable_commands_in_new_shell()
             container = None
             if remote_container is None:
                 container = self._find_container(
@@ -794,11 +796,16 @@ class PulsarJobRunner(AsynchronousJobRunner):
         )
         return client_outputs
 
+    @staticmethod
+    def pulsar_version(remote_job_config):
+        pulsar_version = packaging.version.parse(remote_job_config.get("pulsar_version", "0.6.0"))
+        return pulsar_version
+
     @staticmethod
     def check_job_config(remote_job_config, check_features=None):
         check_features = check_features or {}
         # 0.6.0 was newest Pulsar version that did not report it's version.
-        pulsar_version = packaging.version.parse(remote_job_config.get("pulsar_version", "0.6.0"))
+        pulsar_version = PulsarJobRunner.pulsar_version(remote_job_config)
         needed_version = packaging.version.parse("0.0.0")
         log.info(f"pulsar_version is {pulsar_version}")
         for feature, needed in list(check_features.items()) + [("_default_", True)]:
diff --git a/lib/galaxy/metadata/__init__.py b/lib/galaxy/metadata/__init__.py
index f5d46ed0296..28263746b4f 100644
--- a/lib/galaxy/metadata/__init__.py
+++ b/lib/galaxy/metadata/__init__.py
@@ -137,6 +137,7 @@ class PortableDirectoryMetadataGenerator(MetadataCollectionStrategy):
         job_metadata=None,
         provided_metadata_style=None,
         compute_tmp_dir=None,
+        compute_version_path=None,
         include_command=True,
         max_metadata_value_size=0,
         max_discovered_files=None,
@@ -240,6 +241,8 @@ class PortableDirectoryMetadataGenerator(MetadataCollectionStrategy):
             )
             metadata_params["job_params"] = job.raw_param_dict()
             metadata_params["output_collections"] = output_collections
+            if compute_version_path:
+                metadata_params["compute_version_path"] = compute_version_path
 
         with open(metadata_params_path, "w") as f:
             json.dump(metadata_params, f)
diff --git a/lib/galaxy/metadata/set_metadata.py b/lib/galaxy/metadata/set_metadata.py
index a66783ea4bb..e6495ce67a6 100644
--- a/lib/galaxy/metadata/set_metadata.py
+++ b/lib/galaxy/metadata/set_metadata.py
@@ -208,15 +208,16 @@ def set_metadata_portable(
         outputs_directory = os.path.join(tool_job_working_directory, "outputs")
         if not os.path.exists(outputs_directory):
             outputs_directory = tool_job_working_directory
+        metadata_directory = os.path.join(tool_job_working_directory, "metadata")
 
         # TODO: constants...
         locations = [
+            (metadata_directory, "tool_"),
             (outputs_directory, "tool_"),
             (tool_job_working_directory, ""),
-            (outputs_directory, ""),  # # Pulsar style output directory? Was this ever used - did this ever work?
         ]
         for directory, prefix in locations:
-            if os.path.exists(os.path.join(directory, f"{prefix}stdout")):
+            if directory and os.path.exists(os.path.join(directory, f"{prefix}stdout")):
                 with open(os.path.join(directory, f"{prefix}stdout"), "rb") as f:
                     tool_stdout = f.read(MAX_STDIO_READ_BYTES)
                 with open(os.path.join(directory, f"{prefix}stderr"), "rb") as f:
@@ -261,9 +262,9 @@ def set_metadata_portable(
         else:
             final_job_state = Job.states.ERROR
 
-        version_string_path = os.path.join("outputs", COMMAND_VERSION_FILENAME)
+        default_version_string_path = os.path.join("outputs", COMMAND_VERSION_FILENAME)
+        version_string_path = metadata_params.get("compute_version_path", default_version_string_path)
         version_string = collect_shrinked_content_from_path(version_string_path)
-
         expression_context = ExpressionContext(dict(stdout=tool_stdout[:255], stderr=tool_stderr[:255]))
 
         # Load outputs.
diff --git a/test/functional/tools/version_command_plain.xml b/test/functional/tools/version_command_plain.xml
index 4d3b925624f..33ff70229d6 100644
--- a/test/functional/tools/version_command_plain.xml
+++ b/test/functional/tools/version_command_plain.xml
@@ -18,6 +18,9 @@ cp '$input' '$output'
             <assert_command>
                 <not_has_text text="VERSION"/>
             </assert_command>
+            <assert_command_version>
+                <has_text text="4.0.0" />
+            </assert_command_version>
         </test>
     </tests>
 </tool>
diff --git a/test/integration/test_pulsar_embedded_extended_metadata.py b/test/integration/test_pulsar_embedded_extended_metadata.py
index 2a332b19eb2..f615957a37c 100644
--- a/test/integration/test_pulsar_embedded_extended_metadata.py
+++ b/test/integration/test_pulsar_embedded_extended_metadata.py
@@ -25,6 +25,8 @@ instance = integration_util.integration_module_instance(EmbeddedAndExtendedMetad
 
 test_tools = integration_util.integration_tool_runner(
     [
+        "version_command_plain",
+        "version_command_tool_dir",
         "simple_constructs",
         "metadata_bam",
         # "job_properties",  # https://github.com/galaxyproject/galaxy/issues/11813
diff --git a/test/unit/app/jobs/test_command_factory.py b/test/unit/app/jobs/test_command_factory.py
index 1115a3c35df..3c64e98ade9 100644
--- a/test/unit/app/jobs/test_command_factory.py
+++ b/test/unit/app/jobs/test_command_factory.py
@@ -253,7 +253,11 @@ class MockJobWrapper:
 
     @property
     def job_io(self):
-        return Bunch(get_output_fnames=lambda: ["output1"], check_job_script_integrity=False)
+        return Bunch(
+            get_output_fnames=lambda: ["output1"],
+            check_job_script_integrity=False,
+            version_path=None,
+        )
 
     @property
     def is_cwl_job(self):
diff --git a/test/unit/app/jobs/test_runner_local.py b/test/unit/app/jobs/test_runner_local.py
index 6782d70f9d0..626fdc0818b 100644
--- a/test/unit/app/jobs/test_runner_local.py
+++ b/test/unit/app/jobs/test_runner_local.py
@@ -191,7 +191,9 @@ class MockJobWrapper:
 
     @property
     def job_io(self):
-        return bunch.Bunch(get_output_fnames=lambda: [], check_job_script_integrity=False)
+        return bunch.Bunch(
+            get_output_fnames=lambda: [], check_job_script_integrity=False, version_path="/tmp/version_path"
+        )
 
     def get_job(self):
         return self.job