diff --git a/client/src/components/Workflow/Editor/Index.vue b/client/src/components/Workflow/Editor/Index.vue
index b045017acc9c..64502b77a927 100644
--- a/client/src/components/Workflow/Editor/Index.vue
+++ b/client/src/components/Workflow/Editor/Index.vue
@@ -13,6 +13,7 @@
             @onRefactor="onRefactor"
             @onShow="hideModal" />
         <MessagesModal :title="messageTitle" :message="messageBody" :error="messageIsError" @onHidden="resetMessage" />
+        <SaveChangesModal :nav-url.sync="navUrl" :show-modal.sync="showSaveChangesModal" @on-proceed="onNavigate" />
         <b-modal
             v-model="showSaveAsModal"
             title="Save As a New Workflow"
@@ -147,7 +148,7 @@
     <MarkdownEditor
         v-else
         :markdown-text="markdownText"
-        :markdown-config="markdownConfig"
+        :markdown-config="report"
         mode="report"
         :title="'Workflow Report: ' + name"
         :steps="steps"
@@ -169,7 +170,7 @@
 <script>
 import { Toast } from "composables/toast";
 import { storeToRefs } from "pinia";
-import Vue, { computed, onUnmounted, ref, unref } from "vue";
+import Vue, { computed, nextTick, onUnmounted, ref, unref } from "vue";
 
 import { replaceLabel } from "@/components/Markdown/parse";
 import { getUntypedWorkflowParameters } from "@/components/Workflow/Editor/modules/parameters";
@@ -195,6 +196,7 @@ import WorkflowLint from "./Lint.vue";
 import MessagesModal from "./MessagesModal.vue";
 import WorkflowOptions from "./Options.vue";
 import RefactorConfirmationModal from "./RefactorConfirmationModal.vue";
+import SaveChangesModal from "./SaveChangesModal.vue";
 import StateUpgradeModal from "./StateUpgradeModal.vue";
 import WorkflowGraph from "./WorkflowGraph.vue";
 import MarkdownEditor from "@/components/Markdown/MarkdownEditor.vue";
@@ -207,6 +209,7 @@ export default {
     components: {
         MarkdownEditor,
         FlexPanel,
+        SaveChangesModal,
         StateUpgradeModal,
         ToolPanel,
         FormDefault,
@@ -313,7 +316,6 @@ export default {
     data() {
         return {
             isCanvas: true,
-            markdownConfig: null,
             markdownText: null,
             versions: [],
             parameters: null,
@@ -341,6 +343,8 @@ export default {
             transform: { x: 0, y: 0, k: 1 },
             graphOffset: { left: 0, top: 0, width: 0, height: 0 },
             debounceTimer: null,
+            showSaveChangesModal: false,
+            navUrl: "",
         };
     },
     computed: {
@@ -702,14 +706,21 @@ export default {
             const runUrl = `/workflows/run?id=${this.id}`;
             this.onNavigate(runUrl);
         },
-        async onNavigate(url) {
+        async onNavigate(url, forceSave = false, ignoreChanges = false) {
             if (this.isNewTempWorkflow) {
                 await this.onCreate();
-            } else {
-                await this.onSave(true);
+            } else if (this.hasChanges && !forceSave && !ignoreChanges) {
+                // if there are changes, prompt user to save or discard or cancel
+                this.navUrl = url;
+                this.showSaveChangesModal = true;
+                return;
+            } else if (forceSave) {
+                // when forceSave is true, save the workflow before navigating
+                await this.onSave();
             }
 
             this.hasChanges = false;
+            await nextTick();
             this.$router.push(url);
         },
         onSave(hideProgress = false) {
@@ -787,8 +798,8 @@ export default {
 
             const report = data.report || {};
             const markdown = report.markdown || reportDefault;
+            this.report = report;
             this.markdownText = markdown;
-            this.markdownConfig = report;
             this.hideModal();
             this.stateMessages = getStateUpgradeMessages(data);
             const has_changes = this.stateMessages.length > 0;
diff --git a/client/src/components/Workflow/Editor/SaveChangesModal.vue b/client/src/components/Workflow/Editor/SaveChangesModal.vue
new file mode 100644
index 000000000000..9a2b5bbda2d0
--- /dev/null
+++ b/client/src/components/Workflow/Editor/SaveChangesModal.vue
@@ -0,0 +1,97 @@
+<script setup lang="ts">
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { faSave, faTimes, faTrash } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BButton, BModal } from "bootstrap-vue";
+import { ref } from "vue";
+
+import localize from "@/utils/localization";
+
+library.add(faSave, faTimes, faTrash);
+
+interface Props {
+    /** Show the save changes modal */
+    showModal: boolean;
+    /** The URL to navigate to before saving/ignoring changes */
+    navUrl: string;
+}
+
+const props = withDefaults(defineProps<Props>(), {
+    showModal: false,
+});
+
+const busy = ref(false);
+
+const emit = defineEmits<{
+    /** Proceed with or without saving the changes */
+    (e: "on-proceed", url: string, forceSave: boolean, ignoreChanges: boolean): void;
+    /** Update the nav URL prop */
+    (e: "update:nav-url", url: string): void;
+    /** Update the show modal boolean prop */
+    (e: "update:show-modal", showModal: boolean): void;
+}>();
+
+const title = localize("You have unsaved changes. Do you want to save them before proceeding?");
+const body = localize(
+    "Click 'Save' to save your changes and proceed, 'Don't Save' to discard them and proceed, or 'Cancel' to return to the editor."
+);
+
+const buttonTitles = {
+    cancel: localize("Do not run proceed and return to editor"),
+    dontSave: localize("Discard changes and proceed"),
+    save: localize("Save changes and proceed"),
+};
+
+function closeModal() {
+    emit("update:show-modal", false);
+    emit("update:nav-url", "");
+}
+
+function dontSave() {
+    busy.value = true;
+    emit("on-proceed", props.navUrl, false, true);
+}
+
+function saveChanges() {
+    busy.value = true;
+    closeModal();
+    emit("on-proceed", props.navUrl, true, false);
+}
+</script>
+
+<template>
+    <BModal :title="title" :visible="props.showModal" @close="closeModal" @hide="closeModal">
+        <div>
+            {{ body }}
+        </div>
+        <template v-slot:modal-footer>
+            <BButton
+                v-b-tooltip.noninteractive.hover
+                :title="buttonTitles['cancel']"
+                variant="secondary"
+                :disabled="busy"
+                @click="closeModal">
+                <FontAwesomeIcon :icon="faTimes" />
+                {{ localize("Cancel") }}
+            </BButton>
+            <BButton
+                v-b-tooltip.noninteractive.hover
+                :title="buttonTitles['dontSave']"
+                variant="danger"
+                :disabled="busy"
+                @click="dontSave">
+                <FontAwesomeIcon :icon="faTrash" />
+                {{ localize("Don't Save") }}
+            </BButton>
+            <BButton
+                v-b-tooltip.noninteractive.hover
+                :title="buttonTitles['save']"
+                variant="primary"
+                :disabled="busy"
+                @click="saveChanges">
+                <FontAwesomeIcon :icon="faSave" />
+                {{ localize("Save") }}
+            </BButton>
+        </template>
+    </BModal>
+</template>
diff --git a/client/src/stores/workflowStepStore.ts b/client/src/stores/workflowStepStore.ts
index c696f3141ad9..e1ee49f479df 100644
--- a/client/src/stores/workflowStepStore.ts
+++ b/client/src/stores/workflowStepStore.ts
@@ -340,6 +340,7 @@ export const useWorkflowStepStore = defineScopedStore("workflowStepStore", (work
 
         del(steps.value, stepId.toString());
         del(stepExtraInputs.value, stepId);
+        del(stepMapOver.value, stepId.toString());
     }
 
     return {
diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 2100c81f8cae..f3021dc25d48 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -1453,7 +1453,7 @@
     This option has no effect if the file specified by
     object_store_config_file exists. Otherwise, if this option is set,
     it overrides any other objectstore settings.
-    The syntax, available instrumenters, and documentation of their
+    The syntax, available storage plugins, and documentation of their
     options is explained in detail in the object store sample
     configuration file, `object_store_conf.sample.yml`
 :Default: ``None``
@@ -2606,8 +2606,20 @@
 
 :Description:
     The upload store is a temporary directory in which files uploaded
-    by the tus middleware or server will be placed. Defaults to
-    new_file_path if not set.
+    by the tus middleware or server for user uploads will be placed.
+    Defaults to new_file_path if not set.
+:Default: ``None``
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``tus_upload_store_job_files``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    The upload store is a temporary directory in which files uploaded
+    by the tus middleware or server for remote job files (Pulsar) will
+    be placed. Defaults to tus_upload_store if not set.
 :Default: ``None``
 :Type: str
 
@@ -4030,6 +4042,23 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~~~~
+``oidc_scope_prefix``
+~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Sets the prefix for OIDC scopes specific to this Galaxy instance.
+    If an API call is made against this Galaxy instance using an OIDC
+    bearer token, any scopes must be prefixed with this value e.g.
+    https://galaxyproject.org/api. More concretely, to request all
+    permissions that the user has, the scope would have to be
+    specified as "<prefix>:*". e.g "https://galaxyproject.org/api:*".
+    Currently, only * is recognised as a valid scope, and future
+    iterations may provide more fine-grained scopes.
+:Default: ``https://galaxyproject.org/api``
+:Type: str
+
+
 ~~~~~~~~~~~~~~~~~~~~
 ``auth_config_file``
 ~~~~~~~~~~~~~~~~~~~~
@@ -5439,9 +5468,9 @@
 :Type: str
 
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``help_forum_tool_panel_integration_enabled``
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``enable_help_forum_tool_panel_integration``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 :Description:
     Enable the integration of the Galaxy Help Forum in the tool panel.
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index 96c2a84e0bda..21b325bdb490 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -1,21 +1,21 @@
 # Galaxy is configured by default to be usable in a single-user development
 # environment.  To tune the application for a multi-user production
 # environment, see the documentation at:
-#
+# 
 #  https://docs.galaxyproject.org/en/master/admin/production.html
-#
+# 
 # Throughout this sample configuration file, except where stated otherwise,
 # uncommented values override the default if left unset, whereas commented
 # values are set to the default value.  Relative paths are relative to the root
 # Galaxy directory.
-#
+# 
 # Examples of many of these options are explained in more detail in the Galaxy
 # Community Hub.
-#
+# 
 #   https://galaxyproject.org/admin/config
-#
+# 
 # Config hackers are encouraged to check there before asking for help.
-#
+# 
 # Configuration for Gravity process manager.
 # ``uwsgi:`` section will be ignored if Galaxy is started via Gravity commands (e.g ``./run.sh``, ``galaxy`` or ``galaxyctl``).
 gravity:
@@ -181,7 +181,7 @@ gravity:
     # enable: false
 
     # gx-it-proxy version
-    # version: '>=0.0.5'
+    # version: '>=0.0.6'
 
     # Public-facing IP of the proxy
     # ip: localhost
@@ -248,6 +248,14 @@ gravity:
     # Must match ``tus_upload_store`` setting in ``galaxy:`` section.
     # upload_dir:
 
+    # Value of tusd -hooks-httpd option
+    #
+    # the default of is suitable for using tusd for Galaxy uploads and should not be changed unless you are using tusd for
+    # other purposes such as Pulsar staging.
+    #
+    # The value of galaxy_infrastructure_url is automatically prepended if the option starts with a `/`
+    # hooks_http: /api/upload/hooks
+
     # Comma-separated string of enabled tusd hooks.
     #
     # Leave at the default value to require authorization at upload creation time.
@@ -333,15 +341,9 @@ gravity:
     # names.
     # environment: {}
 
-  # Configure dynamic handlers in this section. Below is a simple example
+  # Configure dynamic handlers in this section.
   # See https://docs.galaxyproject.org/en/latest/admin/scaling.html#dynamically-defined-handlers for details.
-  #handlers:
-  #  handler:
-  #    processes: 3
-  #    pools:
-  #      - job-handlers
-  #      - workflow-schedulers
-
+  # handlers: {}
 galaxy:
 
   # The directory that will be prepended to relative paths in options
@@ -1030,7 +1032,7 @@ galaxy:
   # This option has no effect if the file specified by
   # object_store_config_file exists. Otherwise, if this option is set,
   # it overrides any other objectstore settings.
-  # The syntax, available instrumenters, and documentation of their
+  # The syntax, available storage plugins, and documentation of their
   # options is explained in detail in the object store sample
   # configuration file, `object_store_conf.sample.yml`
   #object_store_config: null
@@ -1067,6 +1069,13 @@ galaxy:
   # for that object store entry.
   #object_store_cache_size: -1
 
+  # Set this to true to indicate in the UI that a user's object store
+  # selection isn't simply a "preference" that job destinations often
+  # respect but in fact will always be respected. This should be set to
+  # true to simplify the UI as long as job destinations never override
+  # 'object_store_id's for a jobs.
+  #object_store_always_respect_user_selection: false
+
   # What Dataset attribute is used to reference files in an ObjectStore
   # implementation, this can be 'uuid' or 'id'. The default will depend
   # on how the object store is configured, starting with 20.05 Galaxy
@@ -1304,9 +1313,6 @@ galaxy:
   # The value of this option will be resolved with respect to
   # <data_dir>.
   #interactivetools_map: interactivetools_map.sqlite
-  # Note: the following config should still be used due to lack of
-  # support of data_dir resolution in gx-it-proxy and gravity:
-  #interactivetools_map: database/interactivetools_map.sqlite
 
   # Prefix to use in the formation of the subdomain or path for
   # interactive tools
@@ -1547,10 +1553,15 @@ galaxy:
   #nginx_upload_job_files_path: null
 
   # The upload store is a temporary directory in which files uploaded by
-  # the tus middleware or server will be placed. Defaults to
-  # new_file_path if not set.
+  # the tus middleware or server for user uploads will be placed.
+  # Defaults to new_file_path if not set.
   #tus_upload_store: null
 
+  # The upload store is a temporary directory in which files uploaded by
+  # the tus middleware or server for remote job files (Pulsar) will be
+  # placed. Defaults to tus_upload_store if not set.
+  #tus_upload_store_job_files: null
+
   # Galaxy can upload user files in chunks without using nginx. Enable
   # the chunk uploader by specifying a chunk size larger than 0. The
   # chunk size is specified in bytes (default: 10MB).
@@ -2189,12 +2200,13 @@ galaxy:
   # <config_dir>.
   #oidc_backends_config_file: oidc_backends_config.xml
 
-  # Sets the prefix for OIDC scopes specific to this Galaxy instance.
-  # If an API call is made against this Galaxy instance using an OIDC bearer token,
-  # any scopes must be prefixed with this value e.g. https://galaxyproject.org/api.
-  # More concretely, to request all permissions that the user has, the scope
-  # would have to be specified as "<prefix>:*". e.g "https://galaxyproject.org/api:*".
-  # Currently, only * is recognised as a valid scope, and future iterations may
+  # Sets the prefix for OIDC scopes specific to this Galaxy instance. If
+  # an API call is made against this Galaxy instance using an OIDC
+  # bearer token, any scopes must be prefixed with this value e.g.
+  # https://galaxyproject.org/api. More concretely, to request all
+  # permissions that the user has, the scope would have to be specified
+  # as "<prefix>:*". e.g "https://galaxyproject.org/api:*". Currently,
+  # only * is recognised as a valid scope, and future iterations may
   # provide more fine-grained scopes.
   #oidc_scope_prefix: https://galaxyproject.org/api
 
@@ -2897,3 +2909,4 @@ galaxy:
   # Enable the integration of the Galaxy Help Forum in the tool panel.
   # This requires the help_forum_api_url to be set.
   #enable_help_forum_tool_panel_integration: false
+
diff --git a/scripts/update_cwl_conformance_tests.sh b/scripts/update_cwl_conformance_tests.sh
index 2a71267c554e..4cc2cdc1386d 100755
--- a/scripts/update_cwl_conformance_tests.sh
+++ b/scripts/update_cwl_conformance_tests.sh
@@ -17,11 +17,7 @@ for version in $VERSIONS; do
         conformance_filepath=conformance_tests.yaml
         tests_dir=tests
     fi
-    if [ "$version" = '1.2' ]; then
-	branch=1.2.1_proposed
-    else
-	branch=main
-    fi
+    branch=main
     wget "https://github.com/common-workflow-language/${repo_name}/archive/${branch}.zip"
     unzip ${branch}.zip
     rm -rf "${DEST_DIR}/v${version}"