diff --git a/src/Core/BaseKernel.php b/src/Core/BaseKernel.php
index f321d288a..a3893ab9d 100644
--- a/src/Core/BaseKernel.php
+++ b/src/Core/BaseKernel.php
@@ -21,7 +21,6 @@ use SilverStripe\Core\Manifest\ClassManifest;
 use SilverStripe\Core\Manifest\ModuleLoader;
 use SilverStripe\Core\Manifest\ModuleManifest;
 use SilverStripe\Dev\DebugView;
-use SilverStripe\Dev\Deprecation;
 use SilverStripe\Logging\ErrorHandler;
 use SilverStripe\View\PublicThemes;
 use SilverStripe\View\SSViewer;
@@ -179,26 +178,17 @@ abstract class BaseKernel implements Kernel
      */
     protected function bootManifests($flush)
     {
-        // Setup autoloader
-        $ignoredCIConfigs = Deprecation::withNoReplacement(function () {
-            return $this->getIgnoredCIConfigs();
-        });
-
-        Deprecation::withNoReplacement(function () use ($flush, $ignoredCIConfigs) {
-            $this->getClassLoader()->init(
-                $this->getIncludeTests(),
-                $flush,
-                $ignoredCIConfigs
-            );
-
-            // Find modules
-            $this->getModuleLoader()->init(
-                $this->getIncludeTests(),
-                $flush,
-                $ignoredCIConfigs
-            );
-        });
+        $this->getClassLoader()->init(
+            $this->getIncludeTests(),
+            $flush
+        );
 
+        // Find modules
+        $this->getModuleLoader()->init(
+            $this->getIncludeTests(),
+            $flush
+        );
+        
         // Flush config
         if ($flush) {
             $config = $this->getConfigLoader()->getManifest();
@@ -215,13 +205,10 @@ abstract class BaseKernel implements Kernel
             $defaultSet->setProject(
                 ModuleManifest::config()->get('project')
             );
-            Deprecation::withNoReplacement(function () use ($defaultSet, $flush, $ignoredCIConfigs) {
-                $defaultSet->init(
-                    $this->getIncludeTests(),
-                    $flush,
-                    $ignoredCIConfigs
-                );
-            });
+            $defaultSet->init(
+                $this->getIncludeTests(),
+                $flush
+            );
         }
     }
 
@@ -230,15 +217,8 @@ abstract class BaseKernel implements Kernel
      */
     protected function bootConfigs()
     {
-        global $project;
-        $projectBefore = $project;
-        $config = ModuleManifest::config();
         // After loading all other app manifests, include _config.php files
         $this->getModuleLoader()->getManifest()->activateConfig();
-        if ($project && $project !== $projectBefore) {
-            Deprecation::notice('5.0', '$project global is deprecated');
-            $config->set('project', $project);
-        }
     }
 
     /**
diff --git a/src/Core/Manifest/ClassLoader.php b/src/Core/Manifest/ClassLoader.php
index 5c1fabbe1..d8386c5e4 100644
--- a/src/Core/Manifest/ClassLoader.php
+++ b/src/Core/Manifest/ClassLoader.php
@@ -2,9 +2,6 @@
 
 namespace SilverStripe\Core\Manifest;
 
-use SilverStripe\Core\ClassInfo;
-use SilverStripe\Dev\Deprecation;
-
 /**
  * A class that handles loading classes and interfaces from a class manifest
  * instance.
@@ -126,24 +123,9 @@ class ClassLoader
         foreach ($this->manifests as $manifest) {
             /** @var ClassManifest $instance */
             $instance = $manifest['instance'];
-            Deprecation::withNoReplacement(function () use ($instance, $includeTests, $forceRegen, $ignoredCIConfigs) {
-                $instance->init($includeTests, $forceRegen, $ignoredCIConfigs);
-            });
+            $instance->init($includeTests, $forceRegen);
         }
 
         $this->registerAutoloader();
     }
-
-    /**
-     * Returns true if a class or interface name exists in the manifest.
-     *
-     * @param  string $class
-     * @return bool
-     * @deprecated 4.0.1 Use ClassInfo::exists() instead
-     */
-    public function classExists($class)
-    {
-        Deprecation::notice('4.0.1', 'Use ClassInfo::exists() instead');
-        return ClassInfo::exists($class);
-    }
 }
diff --git a/src/Core/Manifest/ClassManifest.php b/src/Core/Manifest/ClassManifest.php
index 62533ca6f..9d406620d 100644
--- a/src/Core/Manifest/ClassManifest.php
+++ b/src/Core/Manifest/ClassManifest.php
@@ -291,9 +291,7 @@ class ClassManifest
         }
 
         // Build
-        Deprecation::withNoReplacement(function () use ($includeTests, $ignoredCIConfigs) {
-            $this->regenerate($includeTests, $ignoredCIConfigs);
-        });
+        $this->regenerate($includeTests);
     }
 
     /**