diff --git a/client/src/components/Toolshed/InstalledList/Index.vue b/client/src/components/Toolshed/InstalledList/Index.vue
index 5cd31cedf64..5f61b916b61 100644
--- a/client/src/components/Toolshed/InstalledList/Index.vue
+++ b/client/src/components/Toolshed/InstalledList/Index.vue
@@ -33,9 +33,7 @@
                     <template v-slot:cell(name)="row">
                         <b-link href="#" role="button" class="font-weight-bold" @click="row.toggleDetails">
                             <div v-if="!isLatest(row.item)">
-                                <b-badge variant="danger" class="mb-2">
-                                    Newer version available!
-                                </b-badge>
+                                <b-badge variant="danger" class="mb-2"> Newer version available! </b-badge>
                             </div>
                             <div class="name">{{ row.item.name }}</div>
                         </b-link>
@@ -49,9 +47,7 @@
                     No matching entries found for: <span class="font-weight-bold">{{ this.filter }}</span
                     >.
                 </div>
-                <div v-if="showNotAvailable">
-                    No installed repositories found.
-                </div>
+                <div v-if="showNotAvailable">No installed repositories found.</div>
             </div>
         </div>
     </div>
@@ -123,7 +119,7 @@ export default {
         load() {
             this.loading = true;
             this.services
-                .getInstalledRepositories()
+                .getInstalledRepositories({ selectLatest: true })
                 .then((repositories) => {
                     this.repositories = repositories;
                     this.nRepositories = repositories.length;
diff --git a/client/src/components/Toolshed/services.js b/client/src/components/Toolshed/services.js
index 0aab5f52fc9..0c78f080134 100644
--- a/client/src/components/Toolshed/services.js
+++ b/client/src/components/Toolshed/services.js
@@ -78,7 +78,7 @@ export class Services {
         const url = `${getAppRoot()}api/tool_shed_repositories/?uninstalled=False`;
         try {
             const response = await axios.get(url);
-            const repositories = this._groupByNameOwner(response.data, options.filter);
+            const repositories = this._groupByNameOwner(response.data, options.filter, options.selectLatest);
             this._fixToolshedUrls(repositories, Galaxy.config.tool_shed_urls);
             return repositories;
         } catch (e) {
@@ -125,7 +125,19 @@ export class Services {
             rethrowSimple(e);
         }
     }
-    _groupByNameOwner(incoming, filter) {
+    _groupByNameOwner(incoming, filter, selectLatest) {
+        if (selectLatest) {
+            const getSortValue = (x, y) => {
+                return x == y ? 0 : x < y ? -1 : 1;
+            };
+            incoming = incoming.sort((a, b) => {
+                return (
+                    getSortValue(a.name, b.name) ||
+                    getSortValue(a.owner, b.owner) ||
+                    getSortValue(parseInt(b.ctx_rev), parseInt(a.ctx_rev))
+                );
+            });
+        }
         const hash = {};
         const repositories = [];
         incoming.forEach((x) => {
diff --git a/client/src/components/Toolshed/services.test.js b/client/src/components/Toolshed/services.test.js
index ba17d54b19a..ed3d573bffd 100644
--- a/client/src/components/Toolshed/services.test.js
+++ b/client/src/components/Toolshed/services.test.js
@@ -8,6 +8,7 @@ describe("Toolshed service helpers", () => {
             status: "status_0_0",
             description: "description_0_0",
             tool_shed: "url_1",
+            ctx_rev: "1",
         },
         {
             name: "name_0",
@@ -15,6 +16,7 @@ describe("Toolshed service helpers", () => {
             status: "status_0_1",
             description: "description_0_1",
             tool_shed: "url_1",
+            ctx_rev: "3",
         },
         {
             name: "name_1",
@@ -22,6 +24,7 @@ describe("Toolshed service helpers", () => {
             status: "status_1",
             description: "description_1",
             tool_shed: "url_2",
+            ctx_rev: "42",
         },
         {
             name: "name_2",
@@ -29,6 +32,7 @@ describe("Toolshed service helpers", () => {
             status: "Installed",
             description: "description_2",
             tool_shed: "url_2",
+            ctx_rev: "1",
         },
     ];
     const urls = ["http://url_1.com", "http://url_2.com"];
@@ -36,11 +40,12 @@ describe("Toolshed service helpers", () => {
     it("test fix toolshed helper", () => {
         const services = new Services();
         const filter = (x) => x.status !== "Installed";
-        const grouped = services._groupByNameOwner(incoming, filter);
+        const grouped = services._groupByNameOwner(incoming, filter, true);
         services._fixToolshedUrls(grouped, urls);
         expect(grouped.length).toBe(2);
         expect(grouped[0].name).toBe("name_0");
         expect(grouped[0].tool_shed_url).toBe("http://url_1.com");
+        expect(grouped[0].ctx_rev).toBe("3");
         expect(grouped[1].name === "name_1");
         expect(grouped[1].tool_shed_url).toBe("http://url_2.com");
     });
diff --git a/client/src/mvc/library/library-folder-view.js b/client/src/mvc/library/library-folder-view.js
index 961374b8041..2a9c8719504 100644
--- a/client/src/mvc/library/library-folder-view.js
+++ b/client/src/mvc/library/library-folder-view.js
@@ -66,7 +66,7 @@ var FolderView = Backbone.View.extend({
             is_admin = Galaxy.user.isAdmin();
         }
         var template = this.templateFolderPermissions();
-        this.$el.html(template({ folder: this.model, is_admin: is_admin }));
+        this.$el.html(template({ folder: this.model, is_admin: is_admin, root_path: getAppRoot() }));
 
         var self = this;
         $.get(`${getAppRoot()}api/folders/${self.id}/permissions?scope=current`)
@@ -204,7 +204,7 @@ var FolderView = Backbone.View.extend({
         return _.template(
             `<div class="library_style_container">
                 <div>
-                    <a href="/library/folders/<%= folder.get("parent_id") %>">
+                    <a href="<%- root_path %>library/folders/<%= folder.get("parent_id") %>">
                         <button data-toggle="tooltip" data-placement="top" title="Go back to the parent folder"
                             class="btn btn-secondary primary-button" type="button">
                             <span class="fa fa-caret-left fa-lg"/>
diff --git a/client/src/mvc/library/library-libraryrow-view.js b/client/src/mvc/library/library-libraryrow-view.js
index 279bb590d0a..f405f6aa07d 100644
--- a/client/src/mvc/library/library-libraryrow-view.js
+++ b/client/src/mvc/library/library-libraryrow-view.js
@@ -4,6 +4,7 @@ import Backbone from "backbone";
 import { Toast } from "ui/toast";
 import { getGalaxyInstance } from "app";
 import { linkifyHtmlElements } from "mvc/library/library-util";
+import { getAppRoot } from "onload/loadConfig";
 
 // galaxy library row view
 var LibraryRowView = Backbone.View.extend({
@@ -44,6 +45,7 @@ var LibraryRowView = Backbone.View.extend({
                 library: library,
                 button_config: this.element_visibility_config,
                 edit_mode: this.edit_mode,
+                root_path: getAppRoot(),
             })
         );
         this.$el.show();
@@ -243,7 +245,7 @@ var LibraryRowView = Backbone.View.extend({
                         <td style="color:grey;"><%- library.get("name") %></td>
                     <% } else { %>
                         <td>
-                            <a href="folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a>
+                            <a href="<%- root_path %>library/folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a>
                         </td>
                     <% } %>
                     <% if(library.get("description")) { %>
diff --git a/config/plugins/webhooks/gtn/script.js b/config/plugins/webhooks/gtn/script.js
index b70527daec7..0d98fdaac03 100644
--- a/config/plugins/webhooks/gtn/script.js
+++ b/config/plugins/webhooks/gtn/script.js
@@ -1,7 +1,11 @@
 var gtnWebhookLoaded = false;
 
 function removeOverlay() {
-    document.getElementById("gtn-container").classList.add("d-none");
+    document.getElementById("gtn-container").style.visibility = "hidden";
+}
+
+function showOverlay() {
+    document.getElementById("gtn-container").style.visibility = "visible";
 }
 
 function addIframe() {
@@ -105,7 +109,7 @@ elementReady("#gtn a").then((el) => {
         if (!gtnWebhookLoaded) {
             addIframe();
         } else {
-            document.getElementById("gtn-container").classList.toggle("d-none");
+            showOverlay();
         }
     });
 });
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 89308fe235c..0b474cf047c 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -919,19 +919,26 @@ class JobWrapper(HasResourceParameters):
         if use_persisted_destination:
             self.job_runner_mapper.cached_job_destination = JobDestination(from_job=job)
         # Wrapper holding the info required to restore and clean up from files used for setting metadata externally
-        try:
-            metadata_strategy_override = self.get_destination_configuration('metadata_strategy', None)
-        except JobMappingException:
-            metadata_strategy_override = None
-        if job.tasks:
-            metadata_strategy_override = "directory"
-        self.external_output_metadata = get_metadata_compute_strategy(self.app.config, job.id, metadata_strategy_override=metadata_strategy_override, tool_id=job.tool_id)
+        self.__external_output_metadata = None
+        self.__has_tasks = bool(job.tasks)
 
         self.__commands_in_new_shell = True
         self.__user_system_pwent = None
         self.__galaxy_system_pwent = None
         self.__working_directory = None
 
+    @property
+    def external_output_metadata(self):
+        if self.__external_output_metadata is None:
+            try:
+                metadata_strategy_override = self.get_destination_configuration('metadata_strategy', None)
+            except JobMappingException:
+                metadata_strategy_override = None
+            if self.__has_tasks:
+                metadata_strategy_override = "directory"
+            self.__external_output_metadata = get_metadata_compute_strategy(self.app.config, self.job_id, metadata_strategy_override=metadata_strategy_override, tool_id=self.tool.id)
+        return self.__external_output_metadata
+
     @property
     def _job_dataset_path_rewriter(self):
         if self._dataset_path_rewriter is None:
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index fcaf0ead81b..939dd0a435d 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1158,11 +1158,7 @@ class Job(JobLike, UsesCreateAndUpdateTime, Dictifiable, RepresentById):
         ''', '''
             UPDATE workflow_invocation_step
             SET update_time = :update_time
-            WHERE id in (
-                SELECT workflow_invocation_step.id
-                FROM workflow_invocation_step wis
-                WHERE wis.job_id = :job_id
-            );
+            WHERE job_id = :job_id;
         ''']
         sa_session = object_session(self)
         params = {
@@ -3909,19 +3905,6 @@ class LibraryDatasetDatasetInfoAssociation(RepresentById):
         return True  # always allow inheriting, used for replacement
 
 
-class ValidationError(RepresentById):
-    def __init__(self, message=None, err_type=None, attributes=None):
-        self.message = message
-        self.err_type = err_type
-        self.attributes = attributes
-
-
-class DatasetToValidationErrorAssociation:
-    def __init__(self, dataset, validation_error):
-        self.dataset = dataset
-        self.validation_error = validation_error
-
-
 class ImplicitlyConvertedDatasetAssociation(RepresentById):
 
     def __init__(self, id=None, parent=None, dataset=None, file_type=None, deleted=False, purged=False, metadata_safe=True):
@@ -6170,10 +6153,6 @@ class HistoryTagAssociation(ItemTagAssociation, RepresentById):
     pass
 
 
-class DatasetTagAssociation(ItemTagAssociation, RepresentById):
-    pass
-
-
 class HistoryDatasetAssociationTagAssociation(ItemTagAssociation, RepresentById):
     pass
 
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index d6dc167fcd1..11e84951eca 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -333,14 +333,6 @@ model.ImplicitlyConvertedDatasetAssociation.table = Table(
     Column("metadata_safe", Boolean, index=True, default=True),
     Column("type", TrimmedString(255)))
 
-model.ValidationError.table = Table(
-    "validation_error", metadata,
-    Column("id", Integer, primary_key=True),
-    Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
-    Column("message", TrimmedString(255)),
-    Column("err_type", TrimmedString(64)),
-    Column("attributes", TEXT))
-
 model.Group.table = Table(
     "galaxy_group", metadata,
     Column("id", Integer, primary_key=True),
@@ -1342,16 +1334,6 @@ model.HistoryTagAssociation.table = Table(
     Column("value", TrimmedString(255), index=True),
     Column("user_value", TrimmedString(255), index=True))
 
-model.DatasetTagAssociation.table = Table(
-    "dataset_tag_association", metadata,
-    Column("id", Integer, primary_key=True),
-    Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
-    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
-    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-    Column("user_tname", TrimmedString(255), index=True),
-    Column("value", TrimmedString(255), index=True),
-    Column("user_value", TrimmedString(255), index=True))
-
 model.HistoryDatasetAssociationTagAssociation.table = Table(
     "history_dataset_association_tag_association", metadata,
     Column("id", Integer, primary_key=True),
@@ -1720,8 +1702,6 @@ mapper(model.CloudAuthz, model.CloudAuthz.table, properties=dict(
                    backref='cloudauthz')
 ))
 
-mapper(model.ValidationError, model.ValidationError.table)
-
 simple_mapping(model.DynamicTool)
 
 simple_mapping(model.HistoryDatasetAssociation,
@@ -1785,9 +1765,6 @@ simple_mapping(model.Dataset,
         primaryjoin=(
             (model.Dataset.table.c.id == model.LibraryDatasetDatasetAssociation.table.c.dataset_id) &
             (model.LibraryDatasetDatasetAssociation.table.c.deleted == false()))),
-    tags=relation(model.DatasetTagAssociation,
-        order_by=model.DatasetTagAssociation.table.c.id,
-        backref='datasets')
 )
 
 mapper(model.DatasetHash, model.DatasetHash.table, properties=dict(
@@ -2752,7 +2729,6 @@ def tag_mapping(tag_association_class, backref_name):
 
 
 tag_mapping(model.HistoryTagAssociation, "tagged_histories")
-tag_mapping(model.DatasetTagAssociation, "tagged_datasets")
 tag_mapping(model.HistoryDatasetAssociationTagAssociation, "tagged_history_dataset_associations")
 tag_mapping(model.LibraryDatasetDatasetAssociationTagAssociation, "tagged_library_dataset_dataset_associations")
 tag_mapping(model.PageTagAssociation, "tagged_pages")
diff --git a/lib/galaxy/model/migrate/versions/0169_add_missing_indexes.py b/lib/galaxy/model/migrate/versions/0169_add_missing_indexes.py
new file mode 100644
index 00000000000..a9b56294e59
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0169_add_missing_indexes.py
@@ -0,0 +1,130 @@
+"""
+Migration script to create missing indexes.  Adding new columns to existing tables via SQLAlchemy does not create the index, even if the column definition includes index=True.
+"""
+
+import logging
+
+from sqlalchemy import MetaData
+
+from galaxy.model.migrate.versions.util import (
+    add_index,
+    drop_index
+)
+
+log = logging.getLogger(__name__)
+metadata = MetaData()
+
+indexes = [
+    [
+        "ix_galaxy_user_activation_token",
+        "galaxy_user",
+        "activation_token"
+    ],
+    [
+        "ix_workflow_step_dynamic_tool_id",
+        "workflow_step",
+        "dynamic_tool_id"
+    ],
+    [
+        "ix_history_dataset_association_version",
+        "history_dataset_association",
+        "version"
+    ],
+    [
+        "ix_workflow_invocation_scheduler",
+        "workflow_invocation",
+        "scheduler"
+    ],
+    [
+        "ix_page_slug",
+        "page",
+        "slug"
+    ],
+    [
+        "ix_workflow_invocation_state",
+        "workflow_invocation",
+        "state"
+    ],
+    [
+        "ix_history_dataset_collection_association_implicit_collection_jobs_id",
+        "history_dataset_collection_association",
+        "implicit_collection_jobs_id"
+    ],
+    [
+        "ix_workflow_step_subworkflow_id",
+        "workflow_step",
+        "subworkflow_id"
+    ],
+    [
+        "ix_dynamic_tool_update_time",
+        "dynamic_tool",
+        "update_time"
+    ],
+    [
+        "ix_library_dataset_dataset_association_extended_metadata_id",
+        "library_dataset_dataset_association",
+        "extended_metadata_id"
+    ],
+    [
+        "ix_workflow_invocation_step_implicit_collection_jobs_id",
+        "workflow_invocation_step",
+        "implicit_collection_jobs_id"
+    ],
+    [
+        "ix_workflow_invocation_step_state",
+        "workflow_invocation_step",
+        "state"
+    ],
+    [
+        "ix_workflow_invocation_history_id",
+        "workflow_invocation",
+        "history_id"
+    ],
+    [
+        "ix_workflow_parent_workflow_id",
+        "workflow",
+        "parent_workflow_id"
+    ],
+    [
+        "ix_metadata_file_uuid",
+        "metadata_file",
+        "uuid"
+    ],
+    [
+        "ix_history_dataset_collection_association_job_id",
+        "history_dataset_collection_association",
+        "job_id"
+    ],
+    [
+        "ix_galaxy_user_active",
+        "galaxy_user",
+        "active"
+    ],
+    [
+        "ix_job_dynamic_tool_id",
+        "job",
+        "dynamic_tool_id"
+    ],
+    [
+        "ix_history_dataset_association_extended_metadata_id",
+        "history_dataset_association",
+        "extended_metadata_id"
+    ]
+]
+
+
+def upgrade(migrate_engine):
+    print(__doc__)
+    metadata.bind = migrate_engine
+    metadata.reflect()
+
+    for ix, table, col in indexes:
+        add_index(ix, table, col, metadata)
+
+
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    metadata.reflect()
+
+    for ix, table, col in indexes:
+        drop_index(ix, table, col, metadata)
diff --git a/lib/galaxy/model/migrate/versions/util.py b/lib/galaxy/model/migrate/versions/util.py
index 52010ddc91d..cb6a7d4af82 100644
--- a/lib/galaxy/model/migrate/versions/util.py
+++ b/lib/galaxy/model/migrate/versions/util.py
@@ -1,3 +1,4 @@
+import hashlib
 import logging
 
 from sqlalchemy import (
@@ -47,6 +48,15 @@ def localtimestamp(migrate_engine):
         raise Exception('Unable to convert data for unknown database type: %s' % migrate_engine.name)
 
 
+def truncate_index_name(index_name, engine):
+    # does what sqlalchemy does, see https://github.com/sqlalchemy/sqlalchemy/blob/8455a11bcc23e97afe666873cd872b0f204848d8/lib/sqlalchemy/sql/compiler.py#L4696
+    max_index_name_length = engine.dialect.max_index_name_length or engine.dialect.max_identifier_length
+    if len(index_name) > max_index_name_length:
+        suffix = hashlib.md5(index_name.encode('utf-8')).hexdigest()[-4:]
+        index_name = "{trunc}_{suffix}".format(trunc=index_name[0 : max_index_name_length - 8], suffix=suffix)
+    return index_name
+
+
 def create_table(table):
     try:
         table.create()
@@ -139,6 +149,7 @@ def add_index(index_name, table, column_name, metadata=None, **kwds):
         if not isinstance(table, Table):
             assert metadata is not None
             table = Table(table, metadata, autoload=True)
+        index_name = truncate_index_name(index_name, table.metadata.bind)
         if index_name not in [ix.name for ix in table.indexes]:
             column = table.c[column_name]
             # MySQL cannot index a TEXT/BLOB column without specifying mysql_length
@@ -168,8 +179,9 @@ def drop_index(index, table, column_name=None, metadata=None):
             if not isinstance(table, Table):
                 assert metadata is not None
                 table = Table(table, metadata, autoload=True)
-            if index in [ix.name for ix in table.indexes]:
-                index = Index(index, table.c[column_name])
+            index_name = truncate_index_name(index, table.metadata.bind)
+            if index_name in [ix.name for ix in table.indexes]:
+                index = Index(index_name, table.c[column_name])
             else:
                 log.debug("Index '%s' in table '%s' does not exist.", index, table)
                 return
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index e2a85499999..315a6221fee 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -368,6 +368,9 @@ class ToolBox(BaseGalaxyToolBox):
         # are now using only GALAXY_URL.
         tool_ids = listify(tool_id)
         for tool_id in tool_ids:
+            if tool_id.endswith('/'):
+                # Some data sources send back redirects ending with `/`, this takes care of that case
+                tool_id = tool_id[:-1]
             if get_loaded_tools_by_lineage:
                 tools = toolbox.get_loaded_tools_by_lineage(tool_id)
             else:
diff --git a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
index 0faefdf3e1f..1aabbacfd2a 100644
--- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
@@ -6,7 +6,11 @@ from paste.httpexceptions import (
     HTTPBadRequest,
     HTTPForbidden
 )
-from sqlalchemy import and_
+from sqlalchemy import (
+    and_,
+    cast,
+    Integer,
+)
 
 from galaxy import (
     exceptions,
@@ -82,7 +86,8 @@ class ToolShedRepositoriesController(BaseAPIController):
             clause_list.append(self.app.install_model.ToolShedRepository.table.c.uninstalled == util.asbool(kwd.get('uninstalled')))
         tool_shed_repository_dicts = []
         query = trans.install_model.context.query(self.app.install_model.ToolShedRepository) \
-                                           .order_by(self.app.install_model.ToolShedRepository.table.c.name)
+                                           .order_by(self.app.install_model.ToolShedRepository.table.c.name) \
+                                           .order_by(cast(self.app.install_model.ToolShedRepository.ctx_rev, Integer).desc())
         if len(clause_list) > 0:
             query = query.filter(and_(*clause_list))
         for tool_shed_repository in query.all():
diff --git a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
index 51f77266c40..d7df059f86e 100644
--- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
+++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
@@ -47,9 +47,6 @@ class ToolRunner(BaseUIController):
         # tool id not available, redirect to main page
         if tool_id is None:
             return trans.response.send_redirect(url_for(controller='root', action='welcome'))
-        if tool_id.endswith('/'):
-            # Probably caused by a redirect
-            tool_id = tool_id[:-1]
         tool = self.__get_tool(tool_id)
         # tool id is not matching, display an error
         if not tool: