diff --git a/api/src/org/labkey/api/exp/list/ListService.java b/api/src/org/labkey/api/exp/list/ListService.java
index 9d79a027e38..7d924fcff32 100644
--- a/api/src/org/labkey/api/exp/list/ListService.java
+++ b/api/src/org/labkey/api/exp/list/ListService.java
@@ -51,6 +51,7 @@ static void setInstance(ListService ls)
     boolean hasLists(Container container, boolean includeProjectAndShared);
     ListDefinition createList(Container container, String name, ListDefinition.KeyType keyType);
     ListDefinition createList(Container container, String name, ListDefinition.KeyType keyType, @Nullable TemplateInfo templateInfo, @Nullable ListDefinition.Category category);
+    void deleteLists(Container container, User user, @Nullable String auditUserComment);
     @Nullable ListDefinition getList(Container container, int listId);
     @Nullable ListDefinition getList(Container container, String name);
     @Nullable ListDefinition getList(Container container, String name, boolean includeProjectAndShared);
diff --git a/api/src/org/labkey/api/exp/property/AbstractDomainKind.java b/api/src/org/labkey/api/exp/property/AbstractDomainKind.java
index e14631cbcbd..5ded66b0c70 100644
--- a/api/src/org/labkey/api/exp/property/AbstractDomainKind.java
+++ b/api/src/org/labkey/api/exp/property/AbstractDomainKind.java
@@ -206,7 +206,7 @@ protected boolean getBlanksSql(Domain domain, DomainProperty prop, SQLFragment b
         else
         {
             // Issue 29047
-            blankRowsSQL.appendIdentifier(columnId).append(" IS NOT NULL");
+            blankRowsSQL.appendIdentifier(columnId).append(" IS NULL");
         }
         if (prop.isMvEnabled())
         {
diff --git a/api/src/org/labkey/api/query/QueryService.java b/api/src/org/labkey/api/query/QueryService.java
index f4506494969..1d2205dbdc2 100644
--- a/api/src/org/labkey/api/query/QueryService.java
+++ b/api/src/org/labkey/api/query/QueryService.java
@@ -16,18 +16,38 @@
 
 package org.labkey.api.query;
 
+import jakarta.servlet.http.HttpSession;
 import org.apache.commons.collections4.SetValuedMap;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
 import org.labkey.api.audit.AuditHandler;
 import org.labkey.api.audit.DetailedAuditTypeEvent;
+import org.labkey.api.data.ColumnHeaderType;
+import org.labkey.api.data.ColumnInfo;
+import org.labkey.api.data.CompareType;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerFilter;
+import org.labkey.api.data.DbSchema;
+import org.labkey.api.data.DisplayColumn;
+import org.labkey.api.data.Filter;
+import org.labkey.api.data.JdbcType;
+import org.labkey.api.data.MethodInfo;
+import org.labkey.api.data.MutableColumnInfo;
+import org.labkey.api.data.ParameterDescription;
+import org.labkey.api.data.ParameterDescriptionImpl;
+import org.labkey.api.data.QueryLogging;
+import org.labkey.api.data.Results;
+import org.labkey.api.data.SQLFragment;
+import org.labkey.api.data.Sort;
+import org.labkey.api.data.SqlSelector;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.data.TableSelector;
+import org.labkey.api.data.dialect.SqlDialect;
 import org.labkey.api.gwt.client.model.GWTPropertyDescriptor;
+import org.labkey.api.module.Module;
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.query.column.ColumnInfoTransformer;
-import org.labkey.api.data.*;
-import org.labkey.api.data.dialect.SqlDialect;
-import org.labkey.api.module.Module;
 import org.labkey.api.query.column.ConceptURIColumnInfoTransformer;
 import org.labkey.api.query.snapshot.QuerySnapshotDefinition;
 import org.labkey.api.security.User;
@@ -41,7 +61,6 @@
 import org.labkey.data.xml.TableType;
 import org.springframework.web.servlet.mvc.Controller;
 
-import jakarta.servlet.http.HttpSession;
 import java.io.IOException;
 import java.sql.ResultSet;
 import java.sql.SQLException;
@@ -653,6 +672,13 @@ default MutableColumnInfo applyColumnTransformer(MutableColumnInfo col)
     @Nullable
     ContainerFilter getContainerFilterForLookups(Container container, User user);
 
+    /**
+     * Provides the configured ContainerFilter to utilize when requesting data that is being read
+     * within a folder context. Equivalent to the client side function in @labkey/components
+     */
+    @Nullable
+    ContainerFilter getContainerFilterForFolder(Container container, User user);
+
 
     interface SelectBuilder
     {
diff --git a/api/src/org/labkey/api/study/publish/StudyPublishService.java b/api/src/org/labkey/api/study/publish/StudyPublishService.java
index 027a78aabf9..45b554d9159 100644
--- a/api/src/org/labkey/api/study/publish/StudyPublishService.java
+++ b/api/src/org/labkey/api/study/publish/StudyPublishService.java
@@ -156,7 +156,7 @@ ActionURL publishData(User user, Container sourceContainer, @Nullable Container
 
     String checkForLockedLinks(Dataset def, @Nullable List<Long> rowIds);
 
-    void addRecallAuditEvent(Container sourceContainer, User user, Dataset def, int rowCount, @Nullable Collection<Pair<String,Long>> datasetRowLsidAndSourceRowIds);
+    void addRecallAuditEvent(Container sourceContainer, User user, Dataset def, int rowCount, @Nullable Collection<Long> rowIds);
 
     /**
      * Adds columns to an assay data table, providing a link to any datasets that have
diff --git a/api/src/org/labkey/api/util/XmlBeansUtil.java b/api/src/org/labkey/api/util/XmlBeansUtil.java
index a2617bcd752..f26c2c4c252 100644
--- a/api/src/org/labkey/api/util/XmlBeansUtil.java
+++ b/api/src/org/labkey/api/util/XmlBeansUtil.java
@@ -132,6 +132,7 @@ public static void addComment(XmlTokenSource doc, String comment)
     public static final SAXParserFactory SAX_PARSER_FACTORY_ALLOWING_DOCTYPE;
     public static final XMLInputFactory XML_INPUT_FACTORY;
     public static final DocumentBuilderFactory DOCUMENT_BUILDER_FACTORY;
+    public static final DocumentBuilderFactory DOCUMENT_BUILDER_FACTORY_ALLOWING_DOCTYPE;
 
     static
     {
@@ -145,16 +146,9 @@ public static void addComment(XmlTokenSource doc, String comment)
             SAX_PARSER_FACTORY = saxParserFactory(false);
             SAX_PARSER_FACTORY_ALLOWING_DOCTYPE = saxParserFactory(true);
 
-            //noinspection XMLInputFactory
-            DOCUMENT_BUILDER_FACTORY = DocumentBuilderFactory.newInstance();
-            DOCUMENT_BUILDER_FACTORY.setNamespaceAware(true);
-            DOCUMENT_BUILDER_FACTORY.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
-            DOCUMENT_BUILDER_FACTORY.setFeature("http://xml.org/sax/features/external-general-entities", false);
-            DOCUMENT_BUILDER_FACTORY.setFeature("http://xml.org/sax/features/external-parameter-entities", false);
-            DOCUMENT_BUILDER_FACTORY.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
-            DOCUMENT_BUILDER_FACTORY.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, true);
-            DOCUMENT_BUILDER_FACTORY.setXIncludeAware(false);
-            DOCUMENT_BUILDER_FACTORY.setExpandEntityReferences(false);
+            DOCUMENT_BUILDER_FACTORY = documentBuilderFactory(false);
+            // Use the ALLOWING_DOCTYPE variant when parsing XML that contains a <!DOCTYPE> declaration (e.g. NCBI's eSummary responses)
+            DOCUMENT_BUILDER_FACTORY_ALLOWING_DOCTYPE = documentBuilderFactory(true);
         }
         catch (ParserConfigurationException | SAXException e)
         {
@@ -181,4 +175,26 @@ private static SAXParserFactory saxParserFactory(boolean allowDocType) throws SA
         result.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, true);
         return result;
     }
+
+    private static DocumentBuilderFactory documentBuilderFactory(boolean allowDocType) throws ParserConfigurationException
+    {
+        //noinspection XMLInputFactory
+        DocumentBuilderFactory result = DocumentBuilderFactory.newInstance();
+        result.setNamespaceAware(true);
+
+        // Disable features that could lead to XXE or other vulnerabilities.
+        // When allowDocType is true the DOCTYPE declaration is permitted. External entity
+        // resolution remains disabled, so XXE protection is still in effect.
+        if (!allowDocType)
+        {
+            result.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
+        }
+        result.setFeature("http://xml.org/sax/features/external-general-entities", false);
+        result.setFeature("http://xml.org/sax/features/external-parameter-entities", false);
+        result.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
+        result.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, true);
+        result.setXIncludeAware(false);
+        result.setExpandEntityReferences(false);
+        return result;
+    }
 }
diff --git a/core/src/org/labkey/core/admin/sql/ScriptReorderer.java b/core/src/org/labkey/core/admin/sql/ScriptReorderer.java
index b72cf64d750..7b8110f7f3c 100644
--- a/core/src/org/labkey/core/admin/sql/ScriptReorderer.java
+++ b/core/src/org/labkey/core/admin/sql/ScriptReorderer.java
@@ -118,6 +118,7 @@ public String getReorderedScript(boolean isHtml)
             patterns.add(new SqlPattern("DROP INDEX (IF EXISTS )?\\w+ ON " + TABLE_NAME_REGEX + STATEMENT_ENDING_REGEX, Type.Table, Operation.Other));
 
             patterns.add(new SqlPattern("(CREATE|ALTER) PROCEDURE .+?" + STATEMENT_ENDING_REGEX, Type.NonTable, Operation.Other));
+            patterns.add(new SqlPattern("(CREATE|ALTER) TRIGGER .+?" + "END GO\\s*$", Type.NonTable, Operation.Other));
             patterns.add(new SqlPattern("ALTER TABLE " + TABLE_NAME_REGEX + " CHECK CONSTRAINT " + CONSTRAINT_NAME_REGEX + STATEMENT_ENDING_REGEX, Type.Table, Operation.Other));
         }
         else
diff --git a/core/src/org/labkey/core/admin/sql/SqlScriptController.java b/core/src/org/labkey/core/admin/sql/SqlScriptController.java
index a7868284993..2fe3959e7de 100644
--- a/core/src/org/labkey/core/admin/sql/SqlScriptController.java
+++ b/core/src/org/labkey/core/admin/sql/SqlScriptController.java
@@ -1311,10 +1311,10 @@ protected ActionURL getSaveScriptActionURL(SqlScript script, String newContents,
         - `EXEC core.fn_dropifexists 'MyTable', 'MySchema', 'COLUMN', 'MyColumn` is the same as `ALTER TABLE TableName DROP COLUMN IF EXISTS ColumnName`
         
         Please do the following:
-        - Consolidate all iterative changes (column additions, PK changes, and renames) into the initial CREATE TABLE statements.
+        - Consolidate all iterative changes (column additions & renames, PK changes, and FK changes) into the initial CREATE TABLE statements.
         - Remove unnecessary DROP TABLE statements and core.fn_dropifexists calls, for example, those that come before a table has been created.
         - Remove all intermediate DROP and ALTER statements that are superseded by later logic.
-        - Remove CREATE TABLE and ALTER TABLE statements followed by DROP TABLE or and core.fn_dropifexists 'TABLE' call on that same table.
+        - Remove CREATE TABLE and ALTER TABLE statements followed by DROP TABLE or a core.fn_dropifexists 'TABLE' call on that same table.
         
         Include a summary of the changes you made at the end.
         """;
diff --git a/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java b/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
index 401357afcc1..9b9ed24af05 100644
--- a/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
+++ b/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
@@ -5497,18 +5497,9 @@ public void deleteAllExpObjInContainer(Container c, User user) throws Experiment
             {
                 deleteExperimentRunsByRowIds(c, user, runId);
             }
-            ListService ls = ListService.get();
-            if (ls != null)
-            {
-                for (ListDefinition list : ListService.get().getLists(c, null, false).values())
-                {
-                    // Temporary fix for Issue 21400: **Deleting workbook deletes lists defined in parent container
-                    if (list.getContainer().equals(c))
-                    {
-                        list.delete(user);
-                    }
-                }
-            }
+
+            // Delete lists (because for some reason lists are under the purview of experiment...)
+            ListService.get().deleteLists(c, user, null);
 
             // Delete DataClasses and their exp.Data members
             // Need to delete DataClass before SampleTypes since they may be referenced by the DataClass
diff --git a/issues/src/org/labkey/issue/model/IssueManager.java b/issues/src/org/labkey/issue/model/IssueManager.java
index a2b4bd33d21..d598e313e94 100644
--- a/issues/src/org/labkey/issue/model/IssueManager.java
+++ b/issues/src/org/labkey/issue/model/IssueManager.java
@@ -948,6 +948,11 @@ private static class IndexGroup implements Consumer<SearchService.TaskIndexingQu
         public void accept(SearchService.TaskIndexingQueue a)
         {
             User user = new LimitedUser(UserManager.getGuestUser(), ReaderRole.class);
+            if (IssuesListDefService.get().getRestrictedIssueProvider() != null)
+            {
+                // Pass in an admin user to allow all restricted issues to be indexed by the crawler
+                user = User.getAdminServiceUser();
+            }
             indexIssues(a, user, _ids);
         }
     }
@@ -968,16 +973,9 @@ public static void indexIssues(SearchService.TaskIndexingQueue queue, User user,
 
         for (Integer id : ids)
         {
-            try
-            {
-                IssueObject issue = IssueManager.getIssue(container, user, id);
-                if (issue != null)
-                    queueIssue(queue, id, issue.getProperties(), issue.getCommentObjects());
-            }
-            catch (UnauthorizedException e)
-            {
-                // Issue 51607 ignore restricted issue failures
-            }
+            IssueObject issue = IssueManager.getIssue(container, user, id, false);
+            if (issue != null)
+                queueIssue(queue, id, issue.getProperties(), issue.getCommentObjects());
         }
     }
 
@@ -1015,6 +1013,8 @@ public WebdavResource resolve(@NotNull String resourceIdentifier)
             public HttpView getCustomSearchResult(User user, @NotNull String resourceIdentifier)
             {
                 int issueId;
+                boolean isRestricted = false;       // controls rendering for a restricted issue
+
                 try
                 {
                     issueId = Integer.parseInt(resourceIdentifier);
@@ -1024,23 +1024,34 @@ public HttpView getCustomSearchResult(User user, @NotNull String resourceIdentif
                     return null;
                 }
 
-                final IssueObject issue = getIssue(null, user, issueId, false);
+                IssueObject issue = getIssue(null, user, issueId, false);
                 if (null == issue)
-                    return null;
+                {
+                    if (IssuesListDefService.get().getRestrictedIssueProvider() != null)
+                    {
+                        // allow users to see the summary of a restricted issue, but there will be limited
+                        // information that is rendered.
+                        issue = getIssue(null, User.getAdminServiceUser(), issueId, false);
+                        isRestricted = true;
+                    }
+
+                    if (issue == null)
+                        return null;
+                }
                 Container c = issue.lookupContainer();
                 if (null == c || !c.hasPermission(user, ReadPermission.class))
                     return null;
 
-                return new IssueSummaryView(issue);
+                return new IssueSummaryView(issue, isRestricted);
             }
         };
     }
 
     public static class IssueSummaryView extends JspView
     {
-        IssueSummaryView(IssueObject issue)
+        IssueSummaryView(IssueObject issue, boolean isRestricted)
         {
-            super("/org/labkey/issue/view/searchSummary.jsp", issue);
+            super("/org/labkey/issue/view/searchSummary.jsp", new Pair<>(issue, isRestricted));
         }
     }
 
diff --git a/issues/src/org/labkey/issue/view/searchSummary.jsp b/issues/src/org/labkey/issue/view/searchSummary.jsp
index e8a38dff56e..6ebc4acfc5d 100644
--- a/issues/src/org/labkey/issue/view/searchSummary.jsp
+++ b/issues/src/org/labkey/issue/view/searchSummary.jsp
@@ -23,12 +23,15 @@
 <%@ page import="java.util.regex.Matcher" %>
 <%@ page import="java.util.regex.Pattern" %>
 <%@ page import="org.apache.commons.lang3.Strings" %>
+<%@ page import="org.labkey.api.util.Pair" %>
 <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%
-    JspView<IssueObject> me = HttpView.currentView();
-    final IssueObject issue = me.getModelBean();
+    JspView<Pair<IssueObject, Boolean>> me = HttpView.currentView();
+    final Pair<IssueObject, Boolean> rec = me.getModelBean();
     final User user = getUser();
+    final IssueObject issue = rec.first;
+    final Boolean isRestricted = rec.second;
     final boolean isClosed = Strings.CI.equals(issue.getStatus(),"closed");
     final boolean isOpen = Strings.CI.equals(issue.getStatus(),"open");
 %>
@@ -47,29 +50,36 @@
     <%
         StringBuilder html = new StringBuilder();
         boolean hasTextComment = false;
-        for (IssueObject.CommentObject comment : issue.getCommentObjects())
+        if (isRestricted)
         {
-            String s = comment.getHtmlComment().toString();
-            String pattern1 = "<div class=\"labkey-wiki\">";
-            String pattern2 = "</div>";
-            String regexString = Pattern.quote(pattern1) + "(?s)(.*?)" + Pattern.quote(pattern2);
-            Pattern p = Pattern.compile(regexString);
-            Matcher matcher = p.matcher(s);
-            while (matcher.find())
+            html.append("<div class=\"labkey-error\">Restricted Issue: You do not have access. Contact your administrator for access.</div>");
+        }
+        else
+        {
+            for (IssueObject.CommentObject comment : issue.getCommentObjects())
             {
-                String commentContentText = matcher.group(1);
-                if (!StringUtils.isEmpty(commentContentText))
+                String s = comment.getHtmlComment().toString();
+                String pattern1 = "<div class=\"labkey-wiki\">";
+                String pattern2 = "</div>";
+                String regexString = Pattern.quote(pattern1) + "(?s)(.*?)" + Pattern.quote(pattern2);
+                Pattern p = Pattern.compile(regexString);
+                Matcher matcher = p.matcher(s);
+                while (matcher.find())
                 {
-                    hasTextComment = true;
-                    html.append(commentContentText);
-                    html.append("<br>");
-                    if (html.length() > 500)
-                        break;
+                    String commentContentText = matcher.group(1);
+                    if (!StringUtils.isEmpty(commentContentText))
+                    {
+                        hasTextComment = true;
+                        html.append(commentContentText);
+                        html.append("<br>");
+                        if (html.length() > 500)
+                            break;
+                    }
                 }
             }
         }
 
-    if (hasTextComment) { %>
+    if (hasTextComment && !isRestricted) { %>
         <label style="text-decoration: underline">Comments</label>
     <% } %>
     <div style="max-height:4em; overflow-y:hidden; word-wrap:break-word; white-space: normal; display: -webkit-box; -webkit-line-clamp: 3; -webkit-box-orient: vertical;"><%= unsafe(html.toString()) %></div>
diff --git a/list/src/org/labkey/list/model/ListDefinitionImpl.java b/list/src/org/labkey/list/model/ListDefinitionImpl.java
index dc4fbb7e074..d766c2542dd 100644
--- a/list/src/org/labkey/list/model/ListDefinitionImpl.java
+++ b/list/src/org/labkey/list/model/ListDefinitionImpl.java
@@ -565,37 +565,9 @@ public void delete(User user) throws DomainNotFoundException
     @Override
     public void delete(User user, @Nullable String auditUserComment) throws DomainNotFoundException
     {
-        TableInfo table = getTable(user);
-        QueryUpdateService qus = null;
-
-        if (null != table)
-            qus = table.getUpdateService();
-
-        // In certain cases we may create a list that is not viable (i.e., one in which a table was never created because
-        // the metadata wasn't valid). Still allow deleting the list
-        try (DbScope.Transaction transaction = (table != null) ? table.getSchema().getScope().ensureTransaction() :
-             ExperimentService.get().ensureTransaction())
-        {
-            // remove related full-text search docs and attachments
-            ListManager.get().deleteIndexedList(this);
-            if (qus instanceof ListQueryUpdateService listQus)
-                listQus.deleteRelatedListData(null);
-
-            // then delete the list itself
-            ListManager.get().deleteListDef(getContainer(), getListId());
-            Domain domain = getDomainOrThrow();
-            domain.delete(user, auditUserComment);
-
-            ListManager.get().addAuditEvent(this, user, String.format("The list %s was deleted", _def.getName()));
-
-            transaction.commit();
-        }
-
-        SchemaKey schemaPath = SchemaKey.fromParts(ListQuerySchema.NAME);
-        QueryService.get().fireQueryDeleted(user, getContainer(), null, schemaPath, Collections.singleton(getName()));
+        ListManager.get().deleteList(user, this, auditUserComment);
     }
 
-
     @Override
     public int insertListItems(User user, Container container, List<ListItem> listItems)
     {
diff --git a/list/src/org/labkey/list/model/ListManager.java b/list/src/org/labkey/list/model/ListManager.java
index 497721ba2b4..9637309e819 100644
--- a/list/src/org/labkey/list/model/ListManager.java
+++ b/list/src/org/labkey/list/model/ListManager.java
@@ -16,16 +16,18 @@
 
 package org.labkey.list.model;
 
+import org.apache.commons.collections4.MapUtils;
 import org.apache.commons.collections4.MultiValuedMap;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
-import org.junit.After;
+import org.junit.AfterClass;
 import org.junit.Assert;
-import org.junit.Before;
+import org.junit.BeforeClass;
 import org.junit.Test;
 import org.labkey.api.attachments.AttachmentService;
+import org.labkey.api.attachments.FileAttachmentFile;
 import org.labkey.api.audit.AuditLogService;
 import org.labkey.api.cache.Cache;
 import org.labkey.api.cache.CacheLoader;
@@ -35,6 +37,7 @@
 import org.labkey.api.data.*;
 import org.labkey.api.data.Selector.ForEachBlock;
 import org.labkey.api.exceptions.OptimisticConflictException;
+import org.labkey.api.exp.DomainNotFoundException;
 import org.labkey.api.exp.DomainURIFactory;
 import org.labkey.api.exp.ImportTypesHelper;
 import org.labkey.api.exp.OntologyManager.ImportPropertyDescriptor;
@@ -49,6 +52,7 @@
 import org.labkey.api.exp.property.Domain;
 import org.labkey.api.exp.property.DomainProperty;
 import org.labkey.api.exp.property.PropertyService;
+import org.labkey.api.query.BatchValidationException;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.query.QueryChangeListener;
 import org.labkey.api.query.QueryService;
@@ -57,7 +61,7 @@
 import org.labkey.api.security.User;
 import org.labkey.api.security.UserManager;
 import org.labkey.api.util.ExceptionUtil;
-import org.labkey.api.util.JunitUtil;
+import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.Pair;
 import org.labkey.api.util.Path;
@@ -76,6 +80,7 @@
 import org.labkey.list.view.ListItemAttachmentParent;
 import org.springframework.jdbc.BadSqlGrammarException;
 
+import java.io.File;
 import java.sql.Timestamp;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -453,20 +458,76 @@ private void queryChangeUpdate(User user, Container c, String oldName, String up
         QueryChangeListener.QueryPropertyChange.handleQueryNameChange(oldName, updatedName, new SchemaKey(null, ListQuerySchema.NAME), user, c);
     }
 
-    // CONSIDER: move "list delete" from ListDefinitionImpl.delete() implementation to ListManager for consistency
-    void deleteListDef(Container c, int listid)
+    void deleteList(User user, @NotNull ListDefinitionImpl list, @Nullable String auditUserComment) throws DomainNotFoundException
+    {
+        var table = list.getTable(user);
+        var container = list.getContainer();
+        var listName = list.getName();
+
+        // In certain cases we may create a list that is not viable (i.e., one in which a table was never created because
+        // the metadata wasn't valid). Still allow deleting the list.
+        try (var tx = (table != null) ? table.getSchema().getScope().ensureTransaction() : ExperimentService.get().ensureTransaction())
+        {
+            // remove related full-text search docs and attachments
+            if (table != null && table.getUpdateService() instanceof ListQueryUpdateService qus)
+                qus.deleteRelatedListData(null);
+            else
+                deleteIndexedList(list);
+
+            try
+            {
+                Table.delete(getListMetadataTable(), new Object[]{container, list.getListId()});
+            }
+            catch (OptimisticConflictException x)
+            {
+                // ok
+            }
+            _listDefCache.remove(container.getId());
+
+            list.getDomainOrThrow().delete(user, auditUserComment);
+            addAuditEvent(list, user, String.format("The list %s was deleted", listName));
+
+            tx.commit();
+        }
+
+        QueryService.get().fireQueryDeleted(user, container, null, SchemaKey.fromParts(ListQuerySchema.NAME), Collections.singleton(listName));
+    }
+
+    /**
+     * Deletes all lists and list data in the given container.
+     */
+    public void deleteLists(Container c, User user, @Nullable String auditUserComment)
     {
-        DbScope scope = getListMetadataSchema().getScope();
-        assert scope.isTransactionActive();
         try
         {
-            Table.delete(ListManager.get().getListMetadataTable(), new Object[]{c, listid});
+            var containerId = c.getEntityId().toString();
+            for (var list : ListManager.get().getLists(c, true))
+            {
+                var listDef = ListDefinitionImpl.of(list);
+
+                // Delete the entire list when the list's container is deleted
+                if (containerId.equals(list.getContainerId()))
+                {
+                    deleteList(user, listDef, auditUserComment);
+                    continue;
+                }
+
+                var table = listDef.getTable(user);
+                if (table == null)
+                    continue;
+
+                var qus = table.getUpdateService();
+                if (qus == null)
+                    continue;
+
+                // Otherwise, truncate the rows in this list in this container
+                qus.truncateRows(user, c, null, null);
+            }
         }
-        catch (OptimisticConflictException x)
+        catch (Exception e)
         {
-            // ok
+            throw new RuntimeException(e.getMessage(), e);
         }
-        _listDefCache.remove(c.getId());
     }
 
     public static final SearchService.SearchCategory listCategory = new SearchService.SearchCategory("list", "Lists");
@@ -1264,61 +1325,78 @@ boolean importListSchema(
 
     public static class TestCase extends Assert
     {
+        private static final String PROJECT_NAME = "BiologicsManagerTest Project";
         private static final String LIST_NAME = "Unit Test list";
-        private static final String WORKBOOK1_NAME = "Unit Test Workbook 1";
-        private static final String WORKBOOK2_NAME = "Unit Test Workbook 2";
         private static final String FIELD_NAME = "field";
+        private static final String ATTACHMENT_FIELD_NAME = "attachment";
         private static final String PARENT_LIST_ITEM = "parentItem";
-        private static final String WORKBOOK1_LIST_ITEM = "workbook1Item";
-        private static final String WORKBOOK2_LIST_ITEM = "workbook2Item";
-        private static final Integer PARENT_LI_KEY = 1;
-        private static final Integer WB1_LI_KEY = 2;
-        private static final Integer WB2_LI_KEY = 3;
-
-        private ListDefinitionImpl list;
-        private Container c;
-        private User u;
-        private DomainProperty dp;
-
-        @Before
-        public void setUp() throws Exception
+        private static final String CHILD1_LIST_ITEM = "child1Item";
+        private static final String CHILD2_LIST_ITEM = "child2Item";
+        private static final String KEY_FIELD_NAME = "Unit test list key";
+        private static Integer PARENT_LI_KEY;
+
+        private static ListDefinitionImpl list;
+        private static DomainProperty dp;
+        private static User u;
+        private static Container c;
+
+        @BeforeClass
+        public static void setup() throws Exception
         {
-            JunitUtil.deleteTestContainer();
-            cleanup();
-            c = JunitUtil.getTestContainer();
-            TestContext context = TestContext.get();
-            u = context.getUser();
+            u = TestContext.get().getUser();
+
+            deleteTestContainer();
+
+            c = ContainerManager.ensureContainer(PROJECT_NAME, u);
             list = (ListDefinitionImpl)ListService.get().createList(c, LIST_NAME, ListDefinition.KeyType.AutoIncrementInteger);
-            list.setKeyName("Unit test list Key");
+            list.setKeyName(KEY_FIELD_NAME);
 
             dp = list.getDomain().addProperty();
             dp.setName(FIELD_NAME);
             dp.setType(PropertyService.get().getType(c, PropertyType.STRING.getXmlName()));
             dp.setPropertyURI(ListDomainKind.createPropertyURI(list.getName(), FIELD_NAME, c, list.getKeyType()).toString());
+
+            var attachmentDp = list.getDomain().addProperty();
+            attachmentDp.setName(ATTACHMENT_FIELD_NAME);
+            attachmentDp.setType(PropertyService.get().getType(c, PropertyType.ATTACHMENT.getXmlName()));
+            attachmentDp.setPropertyURI(ListDomainKind.createPropertyURI(list.getName(), ATTACHMENT_FIELD_NAME, c, list.getKeyType()).toString());
             list.save(u);
 
-            addListItem(c, list, PARENT_LIST_ITEM);
+            PARENT_LI_KEY = addListItem(c, list, PARENT_LIST_ITEM, null);
         }
 
-        private void addListItem(Container scopedContainer, ListDefinition scopedList, String value)
+        private static int addListItem(Container scopedContainer, ListDefinition scopedList, String value, @Nullable File attachment) throws Exception
         {
-            List<ListItem> lis = new ArrayList<>();
-            ListItem li = scopedList.createListItem();
-            li.setProperty(dp, value);
-            lis.add(li);
-            list.insertListItems(u, scopedContainer, lis);
+            var row = new CaseInsensitiveHashMap<>();
+            row.put(FIELD_NAME, value);
+            if (attachment != null)
+                row.put(ATTACHMENT_FIELD_NAME, new FileAttachmentFile(attachment));
+
+            var errors = new BatchValidationException();
+            var result = scopedList.getTable(u).getUpdateService().insertRows(u, scopedContainer, List.of(row), errors, null, null);
+            if (errors.hasErrors())
+                throw errors.getLastRowError();
+
+            return MapUtils.getIntValue(result.getFirst(), KEY_FIELD_NAME);
         }
 
-        @After
-        public void tearDown() throws Exception
+        @AfterClass
+        public static void cleanup()
         {
-            cleanup();
+            list = null;
+            dp = null;
+            c = null;
+            u = null;
+
+            deleteTestContainer();
         }
 
-        private void cleanup() throws Exception
+        private static void deleteTestContainer()
         {
-            //TestContext context = TestContext.get();
-            ExperimentService.get().deleteAllExpObjInContainer(c, u);
+            var project = ContainerManager.getForPath(PROJECT_NAME);
+
+            if (project != null)
+                ContainerManager.deleteAll(project, TestContext.get().getUser());
         }
 
         @Test
@@ -1326,39 +1404,81 @@ public void testListServiceInOwnFolder()
         {
             Map<String, ListDefinition> lists = ListService.get().getLists(c);
             assertTrue("Test List not found in own container", lists.containsKey(LIST_NAME));
-            ListItem li = lists.get(LIST_NAME).getListItem(1, u, c);
+            ListItem li = lists.get(LIST_NAME).getListItem(PARENT_LI_KEY, u, c);
             assertEquals("Item not found in own container", PARENT_LIST_ITEM, li.getProperty(dp));
         }
 
         @Test
-        public void testListServiceInWorkbook()
+        public void testListServiceInWorkbook() throws Exception
         {
-            Container workbook1 = setupWorkbook(WORKBOOK1_NAME);
-            Container workbook2 = setupWorkbook(WORKBOOK2_NAME);
+            Container workbook1 = createWorkbook("Unit Test Workbook 1");
+            Container workbook2 = createWorkbook("Unit Test Workbook 2");
             Map<String, ListDefinition> lists = ListService.get().getLists(workbook1);
             assertTrue("Test List not found in workbook", lists.containsKey(LIST_NAME));
 
-            checkListItemScoping(workbook1, workbook2);
+            ListDefinition childList1 = ListService.get().getLists(workbook1).get(LIST_NAME);
+            ListDefinition childList2 = ListService.get().getLists(workbook2).get(LIST_NAME);
+
+            assertEquals("Lists available to each child container are not the same", childList1.toString(), childList2.toString());
+            int childKey1 = addListItem(workbook1, childList1, CHILD1_LIST_ITEM, null);
+            int childKey2 = addListItem(workbook2, childList2, CHILD2_LIST_ITEM, null);
+
+            assertNull("Parent item should not be visible in child container", childList1.getListItem(PARENT_LI_KEY, u, workbook1));
+            assertNull("Sibling child item should not be visible in another child container", childList1.getListItem(childKey2, u, workbook1));
+            assertEquals("Parent container should be able to see child container item", CHILD1_LIST_ITEM, childList1.getListItem(childKey1, u, c).getProperty(dp));
+            assertEquals("Child container should be able to see its own list item", CHILD1_LIST_ITEM, childList1.getListItem(childKey1, u, workbook1).getProperty(dp));
         }
 
-        private Container setupWorkbook(String title)
+        /**
+         * GitHub Issue #1013: Rows added to a list in a subfolder must be cleaned up when that subfolder
+         * is deleted. Previously, those rows were left orphaned in the database.
+         */
+        @Test
+        public void testSubfolderDeletionCleansUpListData() throws Exception
         {
-            return ContainerManager.createContainer(c, null, title, null, WorkbookContainerType.NAME, u);
+            Container subfolder1 = createSubfolder("subfolder1");
+            Container subfolder2 = createSubfolder("subfolder2");
+
+            File attachment1 = FileUtil.createTempFile("subfolder1", ".txt");
+            attachment1.deleteOnExit();
+            File attachment2 = FileUtil.createTempFile("subfolder2", ".txt");
+            attachment2.deleteOnExit();
+
+            int key1 = addListItem(subfolder1, list, "subfolder1Item", attachment1);
+            int key2 = addListItem(subfolder2, list, "subfolder2Item", attachment2);
+
+            // Precondition: parent can see both subfolder items (setUp inserts key 1; subfolders get keys 2 and 3)
+            assertNotNull("Subfolder1 item should be visible from subfolder1 before deletion", list.getListItem(key1, u, subfolder1));
+            assertNotNull("Subfolder2 item should be visible from subfolder2 before deletion", list.getListItem(key2, u, subfolder2));
+
+            TableInfo table = list.getTable(u, c, ContainerFilter.getUnsafeEverythingFilter());
+            assertNotNull("Expected list table to resolve", table);
+
+            // Preverify rows in the database
+            long rowCount = new TableSelector(table, Set.of("Container")).getRowCount();
+            assertEquals("Expected only two rows (parent, subfolder1, subfolder2)", 3, rowCount);
+
+            // Delete subfolder1 — should delete its list rows and attachments,
+            // not touch subfolder2 or the parent or the list definition
+            ListService.get().deleteLists(subfolder1, u, null);
+
+            // Verify row is deleted from underlying table
+            rowCount = new TableSelector(table, Set.of("Container")).getRowCount();
+            assertEquals("Expected only two rows (parent, subfolder2)", 2, rowCount);
+
+            // Items belonging to other containers should be unaffected
+            assertNotNull("Parent item should survive subfolder1 deletion", list.getListItem(PARENT_LI_KEY, u, c));
+            assertNotNull("Subfolder2 item should survive subfolder1 deletion", list.getListItem(key2, u, subfolder2));
         }
 
-        private void checkListItemScoping(Container wb1, Container wb2)
+        private Container createSubfolder(String folderName)
         {
-            ListDefinition wbList1 = ListService.get().getLists(wb1).get(LIST_NAME);
-            ListDefinition wbList2 = ListService.get().getLists(wb2).get(LIST_NAME);
-
-            assertEquals("Lists available to each workbook are not the same", wbList1.toString(), wbList2.toString());
-            addListItem(wb1, wbList1, WORKBOOK1_LIST_ITEM);
-            addListItem(wb2, wbList2, WORKBOOK2_LIST_ITEM);
+            return ContainerManager.createContainer(c, folderName, u);
+        }
 
-            assertNull("Parent item visible in workbook", wbList1.getListItem(PARENT_LI_KEY, u, wb1));
-            assertNull("Sibling workbook item visible in another workbook", wbList1.getListItem(WB2_LI_KEY, u, wb1));
-            assertEquals("Parent container can not see child workbook item", WORKBOOK1_LIST_ITEM, wbList1.getListItem(WB1_LI_KEY, u, c).getProperty(dp));
-            assertEquals("Workbook can not see its own list item", WORKBOOK1_LIST_ITEM, wbList1.getListItem(WB1_LI_KEY, u, wb1).getProperty(dp));
+        private Container createWorkbook(String title)
+        {
+            return ContainerManager.createContainer(c, null, title, null, WorkbookContainerType.NAME, u);
         }
     }
 }
diff --git a/list/src/org/labkey/list/model/ListQueryUpdateService.java b/list/src/org/labkey/list/model/ListQueryUpdateService.java
index b4747339634..9d8502155d4 100644
--- a/list/src/org/labkey/list/model/ListQueryUpdateService.java
+++ b/list/src/org/labkey/list/model/ListQueryUpdateService.java
@@ -35,7 +35,6 @@
 import org.labkey.api.data.DbScope;
 import org.labkey.api.data.LookupResolutionType;
 import org.labkey.api.data.RuntimeSQLException;
-import org.labkey.api.data.Selector.ForEachBatchBlock;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.Table;
 import org.labkey.api.data.TableInfo;
@@ -91,6 +90,7 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Objects;
 import java.util.stream.Collectors;
 
 import static org.labkey.api.util.IntegerUtils.isIntegral;
@@ -761,7 +761,7 @@ protected Map<String, Object> deleteRow(User user, Container container, Map<Stri
         return result;
     }
 
-    record ListRow(Container container, String entityId){}
+    record ListRow(String container, String entityId){}
 
     // Delete attachments and remove documents from the full-text search index. If Container is non-null, delete only
     // from that container (truncate case). If container is null, delete from all containers (delete list case).
@@ -772,27 +772,25 @@ public void deleteRelatedListData(final @Nullable Container container)
 
         if (hasAttachmentProperties())
         {
-            SimpleFilter filter = null != container ? SimpleFilter.createContainerFilter(container) : null;
-
-            // Delete attachments associated with a list in batches of 1,000
-            new TableSelector(getDbTable(), new CsvSet("Container, EntityId"), filter, null).forEachBatch(ListRow.class, 1000, new ForEachBatchBlock<>()
-            {
-                @Override
-                public boolean accept(ListRow row)
-                {
-                    return null != row.entityId();
-                }
-
-                @Override
-                public void exec(List<ListRow> rows)
-                {
-                    // delete the related attachments for this block
-                    AttachmentService.get().deleteAttachments(
-                        rows.stream()
-                            .map(row -> new ListItemAttachmentParent(row.entityId(), row.container()))
-                            .collect(Collectors.toList())
-                    );
-                }
+            var filter = container == null ? new SimpleFilter() : SimpleFilter.createContainerFilter(container);
+            filter.addCondition(FieldKey.fromParts("EntityId"), null, CompareType.NONBLANK);
+
+            // Delete attachments associated with a list in batches
+            new TableSelector(getDbTable(), new CsvSet("Container, EntityId"), filter, null).forEachBatch(ListRow.class, 1_000, rows -> {
+                var containerMap = new HashMap<String, Container>();
+
+                // delete the related attachments for this block
+                AttachmentService.get().deleteAttachments(
+                    rows.stream()
+                        .map(row -> {
+                            var c = containerMap.computeIfAbsent(row.container(), ContainerManager::getForId);
+                            if (c == null)
+                                return null;
+                            return new ListItemAttachmentParent(row.entityId(), c);
+                        })
+                        .filter(Objects::nonNull)
+                        .collect(Collectors.toList())
+                );
             });
         }
     }
diff --git a/list/src/org/labkey/list/model/ListServiceImpl.java b/list/src/org/labkey/list/model/ListServiceImpl.java
index 20d2f33e905..9d93911d038 100644
--- a/list/src/org/labkey/list/model/ListServiceImpl.java
+++ b/list/src/org/labkey/list/model/ListServiceImpl.java
@@ -113,6 +113,12 @@ public ListDefinition createList(Container container, String name, ListDefinitio
         return new ListDefinitionImpl(container, name, keyType, category, templateInfo);
     }
 
+    @Override
+    public void deleteLists(Container container, User user, @Nullable String auditUserComment)
+    {
+        ListManager.get().deleteLists(container, user, auditUserComment);
+    }
+
     @Override
     @Nullable
     public ListDefinition getList(Container container, int listId)
diff --git a/mothership/test/src/org/labkey/test/tests/mothership/MothershipTest.java b/mothership/test/src/org/labkey/test/tests/mothership/MothershipTest.java
index 26ce1e22c4c..7bd1317d08b 100644
--- a/mothership/test/src/org/labkey/test/tests/mothership/MothershipTest.java
+++ b/mothership/test/src/org/labkey/test/tests/mothership/MothershipTest.java
@@ -43,6 +43,7 @@
 import java.util.Arrays;
 import java.util.Date;
 import java.util.List;
+import java.util.function.Supplier;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
@@ -137,9 +138,13 @@ public void testIgnoreExceptionFromDataRegion()
 
         ShowExceptionsPage showExceptionsPage = ShowExceptionsPage.beginAt(this);
         ExceptionSummaryDataRegion exceptionSummary = showExceptionsPage.exceptionSummary();
+        Supplier<List<String>> getAssignedToAndIssue = () -> exceptionSummary.getRowDataAsText(exceptionSummary.getRowIndex(String.valueOf(stackTraceId)), "AssignedTo", "Issue");
+        assertEquals("Exception %d should be unassigned", List.of(" ", " "), getAssignedToAndIssue.get());
+
         exceptionSummary.uncheckAllOnPage();
         exceptionSummary.checkCheckboxByPrimaryKey(stackTraceId);
         exceptionSummary.ignoreSelected();
+        assertEquals("Exception %d should be ignored (issue -1)", List.of(" ", "-1"), getAssignedToAndIssue.get());
 
         StackTraceDetailsPage detailsPage = exceptionSummary.clickStackTrace(stackTraceId);
         assertEquals("Ignoring exception should set GitHub Issue", "-1", detailsPage.githubIssue().get());
diff --git a/pipeline/gradle.properties b/pipeline/gradle.properties
index 7960fca9127..bdf43c99a8c 100644
--- a/pipeline/gradle.properties
+++ b/pipeline/gradle.properties
@@ -1,4 +1,4 @@
-activemqVersion=5.19.2
+activemqVersion=5.19.5
 
 geronimoJ2eeConnector15SpecVersion=1.0.1
 
diff --git a/query/src/org/labkey/query/QueryServiceImpl.java b/query/src/org/labkey/query/QueryServiceImpl.java
index beca1695766..ae6b0fd29df 100644
--- a/query/src/org/labkey/query/QueryServiceImpl.java
+++ b/query/src/org/labkey/query/QueryServiceImpl.java
@@ -3550,6 +3550,40 @@ public ContainerFilter getContainerFilterForLookups(Container container, User us
         return type.create(container, user);
     }
 
+    @Override
+    @Nullable
+    public ContainerFilter getContainerFilterForFolder(Container container, User user)
+    {
+        // Check to see if product folders support is enabled.
+        if (container == null || !container.isProductFoldersEnabled())
+            return null;
+
+        if (isProductFoldersDataListingScopedToProject())
+        {
+            // When requesting data from a top-level folder context the ContainerFilter filters
+            // "down" the folder hierarchy for data.
+            if (container.isProject())
+            {
+                if (isProductFoldersAllFolderScopeEnabled())
+                    return ContainerFilter.Type.AllInProjectPlusShared.create(container, user);
+                return ContainerFilter.Type.CurrentAndSubfoldersPlusShared.create(container, user);
+            }
+
+            // When listing data in a folder scope return data scoped to the current
+            // folder when the experimental feature is enabled.
+            return ContainerFilter.Type.Current.create(container, user);
+        }
+
+        // When requesting data from a top-level folder context the ContainerFilter filters
+        // "down" the folder hierarchy for data.
+        if (container.isProject())
+            return ContainerFilter.Type.CurrentAndSubfoldersPlusShared.create(container, user);
+
+        // When requesting data from a sub-folder context the ContainerFilter filters
+        // "up" the folder hierarchy for data.
+        return ContainerFilter.Type.CurrentPlusProjectAndShared.create(container, user);
+    }
+
     @Override
     @Nullable
     public ContainerFilter.Type getContainerFilterTypeForLookups(Container container)
diff --git a/query/src/org/labkey/query/controllers/QueryMcp.java b/query/src/org/labkey/query/controllers/QueryMcp.java
index b68f2c4ea67..9b11aed43f8 100644
--- a/query/src/org/labkey/query/controllers/QueryMcp.java
+++ b/query/src/org/labkey/query/controllers/QueryMcp.java
@@ -17,6 +17,9 @@
 import org.labkey.api.query.QueryForeignKey;
 import org.labkey.api.query.QueryKey;
 import org.labkey.api.query.QueryParseException;
+import org.labkey.api.query.QueryParseWarning;
+import org.labkey.api.query.QuerySchema;
+import org.labkey.api.query.QueryService;
 import org.labkey.api.query.SchemaKey;
 import org.labkey.api.query.SimpleSchemaTreeVisitor;
 import org.labkey.api.query.UserSchema;
@@ -78,7 +81,7 @@ String listSchemas(ToolContext toolContext)
 
     @Tool(description = "Provide list of tables within the provided schema.")
     @RequiresPermission(ReadPermission.class)
-    String listTables(ToolContext toolContext, @ToolParam(description = "Fully qualified schema name as it would appear in SQL e.g. Study or \"Study.Datasets\"") String schemaName)
+    String listTables(ToolContext toolContext, @ToolParam(description = "Fully qualified schema name as it would appear in SQL e.g. Study or \"Study\".\"Datasets\"") String schemaName)
     {
         var json = _listTables(getContext(toolContext), schemaName);
         return json.toString();
@@ -100,7 +103,7 @@ String listColumns(
     @RequiresPermission(ReadPermission.class)
     String getSourceForSavedQuery(
         ToolContext toolContext,
-        @ToolParam(description = "Fully qualified schema name as it would appear in SQL e.g. Study or \"Study.Datasets\"") String schemaName,
+        @ToolParam(description = "Fully qualified schema name as it would appear in SQL e.g. Study or \"Study\".\"Datasets\"") String schemaName,
         @ToolParam(description = "Table or query name as it would appear in SQL e.g. MyTable, MyQuery, or \"MyTable\"") String queryName
     )
     {
@@ -111,6 +114,49 @@ String getSourceForSavedQuery(
             throw new NotFoundException("Could not find the source for " + schemaName + "." + queryName);
     }
 
+    @Tool(description = "Validate SQL syntax.")
+    @RequiresPermission(ReadPermission.class)
+    String validateSQL(
+            ToolContext toolContext,
+            @ToolParam(description = "Fully qualified schema name as it would appear in SQL e.g. Study or \"Study\".\"Datasets\"") String schemaName,
+            @ToolParam(description = "SQL source") String sql
+    )
+    {
+        var context = getContext(toolContext);
+
+        SchemaKey schemaKey = getSchemaKey(schemaName);
+        QuerySchema schema = DefaultSchema.get(context.getUser(), context.getContainer(), schemaKey);
+
+        try
+        {
+            TableInfo ti = QueryService.get().createTable(schema, sql, null, true);
+            var warnings = ti.getWarnings();
+            if (null != warnings)
+            {
+                var warning = warnings.stream().findFirst();
+                if (warning.isPresent())
+                    throw warning.get();
+            }
+// CONSIDER: add back code to add database validate, but this seems to have stopped working
+//            if (ti.getSqlDialect().isPostgreSQL())
+//            {
+//                var parameters = ti.getNamedParameters();
+//                if (parameters.isEmpty())
+//                {
+//                    SQLFragment sqlPrepare = new SQLFragment("PREPARE validate AS SELECT * FROM ").append(ti.getFromSQL("MYVALIDATEQUERY__"));
+//                    new SqlExecutor(ti.getSchema().getScope()).execute(sqlPrepare);
+//                }
+//            }
+        }
+        catch (Exception x)
+        {
+            // CONSIDER remove line line/character information from DB errors as they won't match the LabKey SQL
+            return "That SQL caused the " + (x instanceof QueryParseWarning ? "warning" : "error") + " below:\n```" + x.getMessage() + "```";
+        }
+        return "success";
+    }
+
+
     /* For now, list all schemas. CONSIDER support incremental querying. */
     public static Map<SchemaKey, UserSchema> _listAllSchemas(DefaultSchema root)
     {
@@ -309,7 +355,7 @@ static String normalizeIdentifier(String compoundIdentifier)
         return new SqlParser().parseIdentifier(compoundIdentifier).toSQLString(true).toLowerCase();
     }
 
-    /** JSON schema example provided by GEMINI, using triple tick-marks to delimit the machine-readable structured data
+    /* JSON schema example provided by GEMINI, using triple tick-marks to delimit the machine-readable structured data
      *
      * Here is the database schema in JSON format:
      * ```{
diff --git a/study/src/org/labkey/study/assay/ExperimentListenerImpl.java b/study/src/org/labkey/study/assay/ExperimentListenerImpl.java
index ece944cc309..ec8c6e027b9 100644
--- a/study/src/org/labkey/study/assay/ExperimentListenerImpl.java
+++ b/study/src/org/labkey/study/assay/ExperimentListenerImpl.java
@@ -15,6 +15,7 @@
  */
 package org.labkey.study.assay;
 
+import org.labkey.api.data.CompareType;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.TableInfo;
@@ -30,8 +31,10 @@
 import org.labkey.api.query.QueryService;
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.query.ValidationException;
+import org.labkey.api.security.ElevatedUser;
 import org.labkey.api.security.User;
 import org.labkey.api.security.permissions.DeletePermission;
+import org.labkey.api.security.roles.ReaderRole;
 import org.labkey.api.study.Dataset;
 import org.labkey.api.study.publish.StudyPublishService;
 import org.labkey.api.view.UnauthorizedException;
@@ -41,6 +44,7 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import static java.util.Collections.singleton;
 
@@ -72,41 +76,58 @@ public void beforeMaterialDelete(List<? extends ExpMaterial> materials, Containe
 
         // It's likely that we'll have multiple materials from the same sample type, so group them for efficient processing
 
-        Map<ExpSampleType, List<ExpMaterial>> typeToMaterials = new HashMap<>();
+        Map<ExpSampleType, Map<Container, List<ExpMaterial>>> typeToMaterials = new HashMap<>();
 
         for (ExpMaterial material: materials)
         {
             ExpSampleType sampleType = material.getSampleType();
             if (sampleType != null)
             {
-                typeToMaterials.computeIfAbsent(sampleType, x -> new ArrayList<>()).add(material);
+                Container materialContainer = material.getContainer();
+                typeToMaterials.
+                        computeIfAbsent(sampleType, k -> new HashMap<>()).
+                        computeIfAbsent(materialContainer, k -> new ArrayList<>()).
+                        add(material);
             }
         }
 
-        for (Map.Entry<ExpSampleType, List<ExpMaterial>> entry : typeToMaterials.entrySet())
+        for (Map.Entry<ExpSampleType, Map<Container, List<ExpMaterial>>> entry : typeToMaterials.entrySet())
         {
             for (Dataset dataset: StudyPublishService.get().getDatasetsForPublishSource(entry.getKey().getRowId(), Dataset.PublishSource.SampleType))
             {
-                TableInfo t = dataset.getTableInfo(user);
-                if (null == t || !t.hasPermission(user, DeletePermission.class))
-                {
-                    throw new UnauthorizedException("Cannot delete rows from dataset " + dataset);
-                }
+                Map<Container, List<ExpMaterial>> containerSamples = entry.getValue();
+
+                // Need Read permission to check for linked samples
+                User userWithReadPerm = ElevatedUser.getElevatedUser(user, ReaderRole.class);
 
-                UserSchema schema = QueryService.get().getUserSchema(user, dataset.getContainer(), "study");
-                TableInfo tableInfo = schema.getTable(dataset.getName());
+                UserSchema schemaWithReadPerm = QueryService.get().getUserSchema(userWithReadPerm, dataset.getContainer(), "study");
+                TableInfo tableInfoForRead = schemaWithReadPerm.getTable(dataset.getName());
+                if (null == tableInfoForRead)
+                    throw new UnauthorizedException("Cannot delete rows from dataset " + dataset);
 
-                // Future optimization - query for all the materials at once
-                for (ExpMaterial material : entry.getValue())
+                for (Map.Entry<Container, List<ExpMaterial>> containerEntry : containerSamples.entrySet())
                 {
-                    SimpleFilter filter = new SimpleFilter(FieldKey.fromParts(ExpMaterialTable.Column.RowId.toString()), material.getRowId());
-                    String lsid = new TableSelector(tableInfo, singleton("LSID"), filter, null).getObject(String.class);
+                    Container sampleContainer = containerEntry.getKey();
+                    List<ExpMaterial> samples = containerEntry.getValue();
+
+                    // GitHub Issue 1028: Can't delete a sample when any sample in the sample type has been linked to study
+                    // check if samples are linked to the dataset, if not, skip the permission check for DeletePermission since we won't be deleting any rows
+                    SimpleFilter filter = new SimpleFilter(FieldKey.fromParts(ExpMaterialTable.Column.RowId.toString()), samples.stream().map(ExpMaterial::getRowId).toList(), CompareType.IN);
+                    Map<String, Object>[] linkedLsidRowIds = new TableSelector(tableInfoForRead, Set.of("LSID", "RowId"), filter, null).getMapArray();
 
-                    if (lsid != null)
+                    Set<String> linkedLsids = Arrays.stream(linkedLsidRowIds).map(m -> (String)m.get("LSID")).collect(java.util.stream.Collectors.toSet());
+                    Set<Long> linkedRowIds = Arrays.stream(linkedLsidRowIds).map(m -> ((Integer)m.get("RowId")).longValue()).collect(java.util.stream.Collectors.toSet());
+                    if (linkedLsids.isEmpty())
+                        continue;
+
+                    TableInfo tableInfo = dataset.getTableInfo(user);
+                    if (null == tableInfo || !tableInfo.hasPermission(user, DeletePermission.class))
                     {
-                        StudyPublishService.get().addRecallAuditEvent(material.getContainer(), user, dataset, 1, null);
-                        dataset.deleteDatasetRows(user, Arrays.asList(lsid));
+                        throw new UnauthorizedException("Cannot delete rows from dataset " + dataset);
                     }
+
+                    StudyPublishService.get().addRecallAuditEvent(sampleContainer, user, dataset, linkedLsids.size(), linkedRowIds);
+                    dataset.deleteDatasetRows(user, linkedLsids);
                 }
             }
         }
diff --git a/study/src/org/labkey/study/assay/StudyPublishManager.java b/study/src/org/labkey/study/assay/StudyPublishManager.java
index 8a30d5c44e7..f0a74f4cbf0 100644
--- a/study/src/org/labkey/study/assay/StudyPublishManager.java
+++ b/study/src/org/labkey/study/assay/StudyPublishManager.java
@@ -1126,6 +1126,11 @@ public void autoLinkDerivedSamples(ExpSampleType sampleType, List<Long> keys, Co
                 qs.setQueryName(sampleType.getName());
                 qs.setBaseFilter(new SimpleFilter().addInClause(FieldKey.fromParts("RowId"), keys));
 
+                // GitHub Issue #901 : lineage sourced subject or timepoint information are not resolving in cross folder configurations
+                ContainerFilter cf = QueryService.get().getContainerFilterForFolder(container, user);
+                if (cf != null)
+                    qs.setContainerFilterName(cf.getType().name());
+
                 Map<StudyPublishService.LinkToStudyKeys, FieldKey> fieldKeyMap = StudyPublishService.get().getSamplePublishFieldKeys(user, container, sampleType, qs);
                 UserSchema userSchema = QueryService.get().getUserSchema(user, container, SamplesSchema.SCHEMA_NAME);
                 QueryView view = new QueryView(userSchema, qs, null);
@@ -1231,10 +1236,11 @@ public void autoLinkSamples(ExpSampleType sampleType, List<Map<FieldKey, Object>
                             for (Map<FieldKey, Object> row : results)
                             {
                                 Object timePointValue = getTimepointValue(row, publishKeys, visitBased, translateMap);
-                                if (row.containsKey(publishKeys.get(LinkToStudyKeys.ParticipantId)) && timePointValue != null)
+                                Object subjectId = row.get(publishKeys.get(LinkToStudyKeys.ParticipantId));
+                                if (subjectId != null  && timePointValue != null)
                                 {
                                     dataMaps.add(Map.of(
-                                            LinkToStudyKeys.ParticipantId.name(), row.get(publishKeys.get(LinkToStudyKeys.ParticipantId)),
+                                            LinkToStudyKeys.ParticipantId.name(), subjectId,
                                             timePointPropName, timePointValue,
                                             StudyPublishService.ROWID_PROPERTY_NAME, row.get(FieldKey.fromParts(StudyPublishService.ROWID_PROPERTY_NAME)),
                                             StudyPublishService.SOURCE_LSID_PROPERTY_NAME, sampleType.getLSID()
@@ -1512,7 +1518,7 @@ public String checkForLockedLinks(Dataset def, @Nullable List<Long> rowIds)
     }
 
     @Override
-    public void addRecallAuditEvent(Container sourceContainer, User user, Dataset def, int rowCount, @Nullable Collection<Pair<String,Long>> pairs)
+    public void addRecallAuditEvent(Container sourceContainer, User user, Dataset def, int rowCount, @Nullable Collection<Long> rowIds)
     {
         Dataset.PublishSource sourceType = def.getPublishSource();
         if (sourceType != null)
@@ -1533,15 +1539,14 @@ public void addRecallAuditEvent(Container sourceContainer, User user, Dataset de
             AuditLogService.get().addEvent(user, event);
 
             // Create sample timeline event for each of the samples
-            if (sourceType == Dataset.PublishSource.SampleType && pairs != null)
+            if (sourceType == Dataset.PublishSource.SampleType && rowIds != null && !rowIds.isEmpty())
             {
                 var timelineEventType = SampleTimelineAuditEvent.SampleTimelineEventType.RECALL;
                 Map<String, Object> eventMetadata = new HashMap<>();
                 eventMetadata.put(SAMPLE_TIMELINE_EVENT_TYPE, timelineEventType.name());
                 String metadata = AbstractAuditTypeProvider.encodeForDataMap(eventMetadata);
 
-                List<Long> sampleIds = pairs.stream().map(Pair::getValue).collect(toList());
-                List<? extends ExpMaterial> samples = ExperimentService.get().getExpMaterials(sampleIds);
+                List<? extends ExpMaterial> samples = ExperimentService.get().getExpMaterials(rowIds);
                 List<AuditTypeEvent> events = new ArrayList<>(samples.size());
                 for (ExpMaterial sample : samples)
                 {
diff --git a/study/src/org/labkey/study/controllers/StudyController.java b/study/src/org/labkey/study/controllers/StudyController.java
index 83b02c438fe..a4674a3a571 100644
--- a/study/src/org/labkey/study/controllers/StudyController.java
+++ b/study/src/org/labkey/study/controllers/StudyController.java
@@ -313,6 +313,7 @@
 import java.util.concurrent.TimeUnit;
 import java.util.function.Predicate;
 import java.util.regex.Pattern;
+import java.util.stream.Collectors;
 
 import static org.labkey.api.util.IntegerUtils.asInteger;
 import static org.labkey.study.model.QCStateSet.PUBLIC_STATES_LABEL;
@@ -3106,9 +3107,10 @@ public boolean handlePost(DeleteDatasetRowsForm form, BindException errors)
                 {
                     String sourceLsid = entry.getKey();
                     Collection<Pair<String, Long>> pairs = entry.getValue();
+                    Collection<Long> rowIds = pairs.stream().map(Pair::getValue).collect(Collectors.toList());
                     Container sourceContainer = publishSource.resolveSourceLsidContainer(sourceLsid, _sourceRowId);
                     if (sourceContainer != null)
-                        StudyPublishService.get().addRecallAuditEvent(sourceContainer, getUser(), _def, pairs.size(), pairs);
+                        StudyPublishService.get().addRecallAuditEvent(sourceContainer, getUser(), _def, pairs.size(), rowIds);
                 }
             }