diff --git a/src/Control/HTTPApplication.php b/src/Control/HTTPApplication.php
index d9c1373ae..d6be9abf6 100644
--- a/src/Control/HTTPApplication.php
+++ b/src/Control/HTTPApplication.php
@@ -6,12 +6,15 @@ use SilverStripe\Control\Middleware\HTTPMiddlewareAware;
 use SilverStripe\Core\Application;
 use SilverStripe\Core\Environment;
 use SilverStripe\Core\Kernel;
+use SilverStripe\Core\Manifest\Module;
 use SilverStripe\Core\Startup\FlushDiscoverer;
 use SilverStripe\Core\Startup\CompositeFlushDiscoverer;
 use SilverStripe\Core\Startup\CallbackFlushDiscoverer;
 use SilverStripe\Core\Startup\RequestFlushDiscoverer;
 use SilverStripe\Core\Startup\ScheduledFlushDiscoverer;
 use SilverStripe\Core\Startup\DeployFlushDiscoverer;
+use SilverStripe\Dev\Deprecation;
+use SilverStripe\GraphQL\TypeCreator;
 
 class HTTPApplication implements Application
 {
@@ -130,6 +133,10 @@ class HTTPApplication implements Application
             return $this->callMiddleware($request, function ($request) use ($callback, $flush) {
                 // Pre-request boot
                 $this->getKernel()->boot($flush);
+
+                // This is the earliest point we can do this and guarantee it's hit exactly once per request.
+                $this->warnAboutDeprecatedSetups();
+
                 return call_user_func($callback, $request);
             });
         } catch (HTTPResponse_Exception $ex) {
@@ -138,4 +145,48 @@ class HTTPApplication implements Application
             $this->getKernel()->shutdown();
         }
     }
+
+    /**
+     * Trigger deprecation notices for legacy configuration which is deprecated but
+     * doesn't have deprecation notices directly on the relevant API
+     *
+     * Don't remove this method even if it's just a no-op - we'll reuse this mechanism
+     * in the future as needed.
+     */
+    private function warnAboutDeprecatedSetups()
+    {
+        // TypeCreator is a class unique to GraphQL v3 - we use it in other areas to detect
+        // which version is being used.
+        if (class_exists(TypeCreator::class)) {
+            Deprecation::notice(
+                '4.13.0',
+                'silverstripe/graphql 3.x is deprecated. Upgrade to 4.x instead.'
+                . ' See https://docs.silverstripe.org/en/4/upgrading/upgrading_to_graphql_4/',
+                Deprecation::SCOPE_GLOBAL
+            );
+        }
+
+        // The alternate_public_dir config property is deprecated, but because it's
+        // always fetched it'll throw a deprecation warning whether you've set it or not.
+        // There are also multiple mechanisms which can result in this bad configuration.
+        if (PUBLIC_DIR !== 'public' || Director::publicDir() !== PUBLIC_DIR) {
+            Deprecation::notice(
+                '4.13.0',
+                'Use of a public webroot other than "public" is deprecated.'
+                . ' See https://docs.silverstripe.org/en/4/changelogs/4.1.0#public-folder/',
+                Deprecation::SCOPE_GLOBAL
+            );
+        }
+
+        // This change of defaults has no other deprecation notice being emitted currently.
+        $project = new Module(BASE_PATH, BASE_PATH);
+        if ($project->getResourcesDir() === '') {
+            Deprecation::notice(
+                '4.13.0',
+                'The RESOURCES_DIR constant will change to "_resources" by default.'
+                . ' See https://docs.silverstripe.org/en/5/changelogs/5.0.0/#api-general',
+                Deprecation::SCOPE_GLOBAL
+            );
+        }
+    }
 }
diff --git a/src/Core/ClassInfo.php b/src/Core/ClassInfo.php
index f127470d3..2e196710a 100644
--- a/src/Core/ClassInfo.php
+++ b/src/Core/ClassInfo.php
@@ -289,14 +289,14 @@ class ClassInfo
      */
     public static function classes_for_file($filePath)
     {
-        $absFilePath = Director::getAbsFile($filePath);
+        $absFilePath = Convert::slashes(Director::getAbsFile($filePath));
         $classManifest = ClassLoader::inst()->getManifest();
         $classes = $classManifest->getClasses();
         $classNames = $classManifest->getClassNames();
 
         $matchedClasses = [];
         foreach ($classes as $lowerClass => $compareFilePath) {
-            if (strcasecmp($absFilePath ?? '', $compareFilePath ?? '') === 0) {
+            if (strcasecmp($absFilePath, Convert::slashes($compareFilePath ?? '')) === 0) {
                 $matchedClasses[$lowerClass] = $classNames[$lowerClass];
             }
         }
@@ -312,14 +312,14 @@ class ClassInfo
      */
     public static function classes_for_folder($folderPath)
     {
-        $absFolderPath = Director::getAbsFile($folderPath);
+        $absFolderPath = Convert::slashes(Director::getAbsFile($folderPath));
         $classManifest = ClassLoader::inst()->getManifest();
         $classes = $classManifest->getClasses();
         $classNames = $classManifest->getClassNames();
 
         $matchedClasses = [];
         foreach ($classes as $lowerClass => $compareFilePath) {
-            if (stripos($compareFilePath ?? '', $absFolderPath ?? '') === 0) {
+            if (stripos(Convert::slashes($compareFilePath ?? ''), $absFolderPath) === 0) {
                 $matchedClasses[$lowerClass] = $classNames[$lowerClass];
             }
         }
diff --git a/src/Core/CustomMethods.php b/src/Core/CustomMethods.php
index 465cb5b07..8841a8c25 100644
--- a/src/Core/CustomMethods.php
+++ b/src/Core/CustomMethods.php
@@ -227,6 +227,7 @@ trait CustomMethods
      *
      * @param object $object
      * @return array
+     * @deprecated 4.13.0 Will be replaced by findMethodsFrom() in CMS 5
      */
     protected function findMethodsFrom($object)
     {
diff --git a/src/Dev/Deprecation.php b/src/Dev/Deprecation.php
index 4f1922b1f..e9b1e7c74 100644
--- a/src/Dev/Deprecation.php
+++ b/src/Dev/Deprecation.php
@@ -10,19 +10,13 @@ use SilverStripe\Core\Injector\InjectorLoader;
 use SilverStripe\Core\Manifest\Module;
 
 /**
- * Handles raising an notice when accessing a deprecated method
+ * Handles raising an notice when accessing a deprecated method, class, configuration, or behaviour.
  *
- * A pattern used in SilverStripe when deprecating a method is to add something like
- *   user_error('This method is deprecated', E_USER_NOTICE);
- * to the method
- *
- * However sometimes we want to mark that a method will be deprecated in some future version and shouldn't be used in
+ * Sometimes we want to mark that a method will be deprecated in some future version and shouldn't be used in
  * new code, but not forbid in the current version - for instance when that method is still heavily used in framework
  * or cms.
  *
- * This class abstracts the above pattern and adds a way to do that.
- *
- * Each call to notice passes a version that the notice will be valid from.
+ * See https://docs.silverstripe.org/en/contributing/release_process/#deprecation
  */
 class Deprecation
 {
@@ -114,6 +108,12 @@ class Deprecation
             $level = 1;
         }
         $newLevel = $level;
+        // handle closures inside withNoReplacement()
+        if (self::$insideWithNoReplacement
+            && substr($backtrace[$newLevel]['function'], -strlen('{closure}')) === '{closure}'
+        ) {
+            $newLevel = $newLevel + 2;
+        }
         // handle call_user_func
         if ($level === 4 && strpos($backtrace[2]['function'] ?? '', 'call_user_func') !== false) {
             $newLevel = 5;
@@ -190,10 +190,10 @@ class Deprecation
                     // Do not add to self::$userErrorMessageBuffer, as the backtrace is too expensive
                     return;
                 }
-    
+
                 // Getting a backtrace is slow, so we only do it if we need it
                 $backtrace = null;
-    
+
                 // Get the calling scope
                 if ($scope == Deprecation::SCOPE_METHOD) {
                     $backtrace = debug_backtrace(0);
@@ -204,7 +204,7 @@ class Deprecation
                 } else {
                     $caller = false;
                 }
-    
+
                 if (substr($string, -1) != '.') {
                     $string .= ".";
                 }
diff --git a/src/ORM/RelatedData/StandardRelatedDataService.php b/src/ORM/RelatedData/StandardRelatedDataService.php
index 04501fc23..c6be4632d 100644
--- a/src/ORM/RelatedData/StandardRelatedDataService.php
+++ b/src/ORM/RelatedData/StandardRelatedDataService.php
@@ -394,14 +394,7 @@ class StandardRelatedDataService implements RelatedDataService
      */
     private function prepareClassNameLiteral(string $value): string
     {
-        $c = chr(92);
-        $escaped = str_replace($c ?? '', "{$c}{$c}", $value ?? '');
-        // postgres
-        if (stripos(get_class(DB::get_conn()), 'postgres') !== false) {
-            return "E'{$escaped}'";
-        }
-        // mysql
-        return "'{$escaped}'";
+        return DB::get_conn()->quoteString($value);
     }
 
     /**
diff --git a/src/i18n/Data/Sources.php b/src/i18n/Data/Sources.php
index 0afc11c46..f6bebdd7a 100644
--- a/src/i18n/Data/Sources.php
+++ b/src/i18n/Data/Sources.php
@@ -24,6 +24,7 @@ class Sources implements Resettable
      *
      * @config
      * @var array
+     * @deprecated 4.0.0 Use SilverStripe\Core\Manifest\ModuleManifest.module_priority instead
      */
     private static $module_priority = [];
 
@@ -35,7 +36,6 @@ class Sources implements Resettable
     public function getSortedModules()
     {
         $sortedModules = [];
-        
         foreach (ModuleLoader::inst()->getManifest()->getModules() as $module) {
             $sortedModules[$module->getName()] = $module->getPath();
         };
diff --git a/src/i18n/TextCollection/i18nTextCollector.php b/src/i18n/TextCollection/i18nTextCollector.php
index db5447983..dc8fc811d 100644
--- a/src/i18n/TextCollection/i18nTextCollector.php
+++ b/src/i18n/TextCollection/i18nTextCollector.php
@@ -457,7 +457,7 @@ class i18nTextCollector
         $this->getWriter()->write(
             $entities,
             $this->defaultLocale,
-            $this->baseSavePath . '/' . $module->getRelativePath()
+            $this->baseSavePath . DIRECTORY_SEPARATOR . $module->getRelativePath()
         );
         return $this;
     }
@@ -511,25 +511,25 @@ class i18nTextCollector
         $modulePath = $module->getPath();
 
         // Search all .ss files in themes
-        if (stripos($module->getRelativePath() ?? '', 'themes/') === 0) {
+        if (stripos($module->getRelativePath() ?? '', 'themes' . DIRECTORY_SEPARATOR) === 0) {
             return $this->getFilesRecursive($modulePath, null, 'ss');
         }
 
         // If non-standard module structure, search all root files
-        if (!is_dir("{$modulePath}/code") && !is_dir("{$modulePath}/src")) {
+        if (!is_dir($modulePath . DIRECTORY_SEPARATOR . 'code') && !is_dir($modulePath . DIRECTORY_SEPARATOR . 'src')) {
             return $this->getFilesRecursive($modulePath);
         }
 
         // Get code files
-        if (is_dir("{$modulePath}/src")) {
-            $files = $this->getFilesRecursive("{$modulePath}/src", null, 'php');
+        if (is_dir($modulePath . DIRECTORY_SEPARATOR . 'src')) {
+            $files = $this->getFilesRecursive($modulePath . DIRECTORY_SEPARATOR . 'src', null, 'php');
         } else {
-            $files = $this->getFilesRecursive("{$modulePath}/code", null, 'php');
+            $files = $this->getFilesRecursive($modulePath . DIRECTORY_SEPARATOR . 'code', null, 'php');
         }
 
         // Search for templates in this module
-        if (is_dir("{$modulePath}/templates")) {
-            $templateFiles = $this->getFilesRecursive("{$modulePath}/templates", null, 'ss');
+        if (is_dir($modulePath . DIRECTORY_SEPARATOR . 'templates')) {
+            $templateFiles = $this->getFilesRecursive($modulePath . DIRECTORY_SEPARATOR . 'templates', null, 'ss');
         } else {
             $templateFiles = $this->getFilesRecursive($modulePath, null, 'ss');
         }
@@ -957,7 +957,7 @@ class i18nTextCollector
             $fileList = [];
         }
         // Skip ignored folders
-        if (is_file("{$folder}/_manifest_exclude") || preg_match($folderExclude ?? '', $folder ?? '')) {
+        if (is_file($folder . DIRECTORY_SEPARATOR . '_manifest_exclude') || preg_match($folderExclude ?? '', $folder ?? '')) {
             return $fileList;
         }
 
diff --git a/tests/php/Dev/DeprecationTest.php b/tests/php/Dev/DeprecationTest.php
index fac1ad726..8b0cf8184 100644
--- a/tests/php/Dev/DeprecationTest.php
+++ b/tests/php/Dev/DeprecationTest.php
@@ -151,6 +151,22 @@ class DeprecationTest extends SapphireTest
         Deprecation::outputNotices();
     }
 
+    public function testNoticeWithNoReplacementTrue()
+    {
+        $message = implode(' ', [
+            'SilverStripe\Dev\Tests\DeprecationTest->testNoticeWithNoReplacementTrue is deprecated.',
+            'My message.',
+            'Called from PHPUnit\Framework\TestCase->runTest.'
+        ]);
+        $this->expectDeprecation();
+        $this->expectDeprecationMessage($message);
+        Deprecation::enable(true);
+        Deprecation::withNoReplacement(function () {
+            Deprecation::notice('123', 'My message.');
+        });
+        Deprecation::outputNotices();
+    }
+
     public function testClassWithNoReplacement()
     {
         $message = implode(' ', [