diff --git a/src/Psalm/Checker/ProjectChecker.php b/src/Psalm/Checker/ProjectChecker.php
index ba6aada8766..da0eee00aae 100644
--- a/src/Psalm/Checker/ProjectChecker.php
+++ b/src/Psalm/Checker/ProjectChecker.php
@@ -231,9 +231,6 @@ public function __construct(
         self::$instance = $this;
 
         $this->cache_provider->use_igbinary = $config->use_igbinary;
-
-        $config->visitStubFiles($this->codebase);
-        $config->initializePlugins($this);
     }
 
     /**
@@ -283,6 +280,8 @@ public function check($base_dir, $is_diff = false)
                 $this->codebase->addFilesToAnalyze([$file_path => $file_path]);
             }
 
+            $this->config->initializePlugins($this);
+
             $this->codebase->scanFiles();
         } else {
             if ($this->debug_output) {
@@ -297,6 +296,8 @@ public function check($base_dir, $is_diff = false)
 
                 $this->checkDiffFilesWithConfig($this->config, $file_list);
 
+                $this->config->initializePlugins($this);
+
                 $this->codebase->scanFiles();
             }
         }
@@ -305,6 +306,8 @@ public function check($base_dir, $is_diff = false)
             echo 'Analyzing files...' . "\n";
         }
 
+        $this->config->visitStubFiles($this->codebase, $this->debug_output);
+
         $this->codebase->analyzer->analyzeFiles($this, $this->threads, $this->alter_code);
 
         $removed_parser_files = $this->cache_provider->deleteOldParserCaches(
@@ -386,8 +389,12 @@ public function checkDir($dir_name)
             echo 'Scanning files...' . "\n";
         }
 
+        $this->config->initializePlugins($this);
+
         $this->codebase->scanFiles();
 
+        $this->config->visitStubFiles($this->codebase, $this->debug_output);
+
         if ($this->output_format === self::TYPE_CONSOLE) {
             echo 'Analyzing files...' . "\n";
         }
@@ -547,8 +554,12 @@ public function checkFile($file_path)
             echo 'Scanning files...' . "\n";
         }
 
+        $this->config->initializePlugins($this);
+
         $this->codebase->scanFiles();
 
+        $this->config->visitStubFiles($this->codebase, $this->debug_output);
+
         if ($this->output_format === self::TYPE_CONSOLE) {
             echo 'Analyzing files...' . "\n";
         }
diff --git a/src/Psalm/Checker/Statements/Expression/Fetch/ArrayFetchChecker.php b/src/Psalm/Checker/Statements/Expression/Fetch/ArrayFetchChecker.php
index b840de04640..72efd970266 100644
--- a/src/Psalm/Checker/Statements/Expression/Fetch/ArrayFetchChecker.php
+++ b/src/Psalm/Checker/Statements/Expression/Fetch/ArrayFetchChecker.php
@@ -635,8 +635,12 @@ public static function getArrayAccessTypeGivenOffset(
 
             if ($type instanceof TNamedObject) {
                 if (strtolower($type->value) !== 'simplexmlelement'
-                    && $codebase->classExists($type->value)
-                    && !$codebase->classImplements($type->value, 'ArrayAccess')
+                    && strtolower($type->value) !== 'arrayaccess'
+                    && (($codebase->classExists($type->value)
+                            && !$codebase->classImplements($type->value, 'ArrayAccess'))
+                        || ($codebase->interfaceExists($type->value)
+                            && !$codebase->interfaceExtends($type->value, 'ArrayAccess'))
+                    )
                 ) {
                     $non_array_types[] = (string)$type;
                 } else {
diff --git a/src/Psalm/Checker/StatementsChecker.php b/src/Psalm/Checker/StatementsChecker.php
index 144275e1452..854fa7c955f 100644
--- a/src/Psalm/Checker/StatementsChecker.php
+++ b/src/Psalm/Checker/StatementsChecker.php
@@ -450,7 +450,9 @@ function ($line) {
                     }
                 }
 
-                if (!$project_checker->codebase->register_global_functions) {
+                if (!$project_checker->codebase->register_stub_files
+                    && !$project_checker->codebase->register_autoload_files
+                ) {
                     $function_id = strtolower($stmt->name->name);
                     $function_context = new Context($context->self);
                     $config = Config::getInstance();
diff --git a/src/Psalm/Codebase.php b/src/Psalm/Codebase.php
index b391e350220..0b90497e376 100644
--- a/src/Psalm/Codebase.php
+++ b/src/Psalm/Codebase.php
@@ -68,12 +68,19 @@ class Codebase
      */
     private static $stubbed_constants = [];
 
+    /**
+     * Whether to register autoloaded information
+     *
+     * @var bool
+     */
+    public $register_autoload_files = false;
+
     /**
      * Whether to log functions just at the file level or globally (for stubs)
      *
      * @var bool
      */
-    public $register_global_functions = false;
+    public $register_stub_files = false;
 
     /**
      * @var bool
@@ -404,7 +411,7 @@ public function getClosureStorage($file_path, $closure_id)
      *
      * @return  void
      */
-    public function addStubbedConstantType($const_id, $type)
+    public function addGlobalConstantType($const_id, Type\Union $type)
     {
         self::$stubbed_constants[$const_id] = $type;
     }
diff --git a/src/Psalm/Codebase/Functions.php b/src/Psalm/Codebase/Functions.php
index a9d752f2508..6471c21599f 100644
--- a/src/Psalm/Codebase/Functions.php
+++ b/src/Psalm/Codebase/Functions.php
@@ -104,7 +104,7 @@ public function getStorage($statements_checker, $function_id)
      *
      * @return void
      */
-    public function addStubbedFunction($function_id, FunctionLikeStorage $storage)
+    public function addGlobalFunction($function_id, FunctionLikeStorage $storage)
     {
         self::$stubbed_functions[strtolower($function_id)] = $storage;
     }
diff --git a/src/Psalm/Codebase/Scanner.php b/src/Psalm/Codebase/Scanner.php
index 8c8028438e1..90c0e8991a0 100644
--- a/src/Psalm/Codebase/Scanner.php
+++ b/src/Psalm/Codebase/Scanner.php
@@ -344,9 +344,13 @@ private function scanFile(
                 $this->queueClassLikeForScanning($fq_classlike_name, $file_path, false, false);
             }
 
-            if ($this->codebase->register_global_functions) {
+            if ($this->codebase->register_autoload_files) {
                 foreach ($file_storage->functions as $function_storage) {
-                    $this->codebase->functions->addStubbedFunction($function_storage->cased_name, $function_storage);
+                    $this->codebase->functions->addGlobalFunction($function_storage->cased_name, $function_storage);
+                }
+
+                foreach ($file_storage->constants as $name => $type) {
+                    $this->codebase->addGlobalConstantType($name, $type);
                 }
             }
         }
diff --git a/src/Psalm/Config.php b/src/Psalm/Config.php
index 3368a9d0fc5..eb3983d4bb6 100644
--- a/src/Psalm/Config.php
+++ b/src/Psalm/Config.php
@@ -1010,11 +1010,13 @@ public function getMockClasses()
     }
 
     /**
+     * @param bool $debug
+     *
      * @return void
      */
-    public function visitStubFiles(Codebase $codebase)
+    public function visitStubFiles(Codebase $codebase, $debug = false)
     {
-        $codebase->register_global_functions = true;
+        $codebase->register_stub_files = true;
 
         // note: don't realpath $generic_stubs_path, or phar version will fail
         $generic_stubs_path = __DIR__ . '/Stubs/CoreGenericFunctions.php';
@@ -1032,16 +1034,21 @@ public function visitStubFiles(Codebase $codebase)
 
         $stub_files = array_merge([$generic_stubs_path, $generic_classes_path], $this->stub_files);
 
-        foreach ($stub_files as $stub_file_path) {
-            $file_storage = $codebase->createFileStorageForPath($stub_file_path);
-            $file_to_scan = new FileScanner($stub_file_path, $this->shortenFileName($stub_file_path), false);
-            $file_to_scan->scan(
-                $codebase,
-                $file_storage
-            );
+        foreach ($stub_files as $file_path) {
+            $codebase->scanner->addFileToShallowScan($file_path);
+        }
+
+        if ($debug) {
+            echo 'Registering stub files' . "\n";
+        }
+
+        $codebase->scanFiles();
+
+        if ($debug) {
+            echo 'Finished registering stub files' . "\n";
         }
 
-        $codebase->register_global_functions = false;
+        $codebase->register_stub_files = false;
     }
 
     /**
@@ -1101,12 +1108,14 @@ public function collectPredefinedFunctions()
     }
 
     /**
+     * @param bool $debug
+     *
      * @return void
      *
      * @psalm-suppress MixedAssignment
      * @psalm-suppress MixedArrayAccess
      */
-    public function visitComposerAutoloadFiles(ProjectChecker $project_checker)
+    public function visitComposerAutoloadFiles(ProjectChecker $project_checker, $debug = false)
     {
         $composer_json_path = $this->base_dir . 'composer.json'; // this should ideally not be hardcoded
 
@@ -1152,15 +1161,23 @@ public function visitComposerAutoloadFiles(ProjectChecker $project_checker)
 
         if ($autoload_files_files) {
             $codebase = $project_checker->codebase;
-            $codebase->register_global_functions = true;
+            $codebase->register_autoload_files = true;
 
             foreach ($autoload_files_files as $file_path) {
-                $codebase->scanner->addFileToShallowScan($file_path);
+                $codebase->scanner->addFileToDeepScan($file_path);
+            }
+
+            if ($debug) {
+                echo 'Registering autoloaded files' . "\n";
             }
 
             $codebase->scanner->scanFiles($codebase->classlikes);
 
-            $project_checker->codebase->register_global_functions = false;
+            if ($debug) {
+                echo 'Finished registering autoloaded files' . "\n";
+            }
+
+            $project_checker->codebase->register_autoload_files = false;
         }
     }
 
diff --git a/src/Psalm/Scanner/FileScanner.php b/src/Psalm/Scanner/FileScanner.php
index e3848155b14..859e2d0fdf8 100644
--- a/src/Psalm/Scanner/FileScanner.php
+++ b/src/Psalm/Scanner/FileScanner.php
@@ -53,6 +53,7 @@ public function scan(
         if ((!$this->will_analyze || $file_storage->deep_scan)
             && $storage_from_cache
             && !$file_storage->has_trait
+            && !$codebase->register_stub_files
         ) {
             return;
         }
diff --git a/src/Psalm/Visitor/DependencyFinderVisitor.php b/src/Psalm/Visitor/DependencyFinderVisitor.php
index 4e9399aaae3..69a795c2c70 100644
--- a/src/Psalm/Visitor/DependencyFinderVisitor.php
+++ b/src/Psalm/Visitor/DependencyFinderVisitor.php
@@ -157,6 +157,8 @@ public function enterNode(PhpParser\Node $node)
         } elseif ($node instanceof PhpParser\Node\Stmt\ClassLike) {
             $class_location = new CodeLocation($this->file_scanner, $node, null, true);
 
+            $storage = null;
+
             if ($node->name === null) {
                 if (!$node instanceof PhpParser\Node\Stmt\Class_) {
                     throw new \LogicException('Anonymous classes are always classes');
@@ -167,34 +169,34 @@ public function enterNode(PhpParser\Node $node)
                 $fq_classlike_name =
                     ($this->aliases->namespace ? $this->aliases->namespace . '\\' : '') . $node->name->name;
 
-                if ($this->codebase->classlike_storage_provider->has($fq_classlike_name)
-                    && !$this->codebase->register_global_functions
-                ) {
-                    $other_file_path = null;
-
-                    try {
-                        $other_file_path = $this->codebase->scanner->getClassLikeFilePath($fq_classlike_name);
-                    } catch (\UnexpectedValueException $e) {
-                        // do nothing
-                    }
-
-                    $duplicate_class_storage = $this->codebase->classlike_storage_provider->get($fq_classlike_name);
+                if ($this->codebase->classlike_storage_provider->has($fq_classlike_name)) {
+                    $duplicate_storage = $this->codebase->classlike_storage_provider->get($fq_classlike_name);
+
+                    if (!$this->codebase->register_stub_files) {
+                        if (!$duplicate_storage->location
+                            || $duplicate_storage->location->file_path !== $this->file_path
+                            || $class_location->getHash() !== $duplicate_storage->location->getHash()
+                        ) {
+                            if (IssueBuffer::accepts(
+                                new DuplicateClass(
+                                    'Class ' . $fq_classlike_name . ' has already been defined'
+                                        . ($duplicate_storage->location
+                                            ? ' in ' . $duplicate_storage->location->file_path
+                                            : ''),
+                                    new CodeLocation($this->file_scanner, $node, null, true)
+                                )
+                            )) {
+                                $this->file_storage->has_visitor_issues = true;
+                            }
 
-                    if (!$duplicate_class_storage->location
-                        || $duplicate_class_storage->location->file_path !== $this->file_path
-                        || $class_location->getHash() !== $duplicate_class_storage->location->getHash()
-                    ) {
-                        if (IssueBuffer::accepts(
-                            new DuplicateClass(
-                                'Class ' . $fq_classlike_name . ' has already been defined'
-                                    . ($other_file_path ? ' in ' . $other_file_path : ''),
-                                new CodeLocation($this->file_scanner, $node, null, true)
-                            )
-                        )) {
-                            $this->file_storage->has_visitor_issues = true;
+                            return PhpParser\NodeTraverser::STOP_TRAVERSAL;
                         }
-
-                        return PhpParser\NodeTraverser::STOP_TRAVERSAL;
+                    } elseif ($duplicate_storage->location
+                        && ($duplicate_storage->location->file_path !== $this->file_path
+                            || $class_location->getHash() !== $duplicate_storage->location->getHash())
+                    ) {
+                        // we're overwriting some methods
+                        $storage = $duplicate_storage;
                     }
                 }
             }
@@ -205,11 +207,13 @@ public function enterNode(PhpParser\Node $node)
 
             $this->fq_classlike_names[] = $fq_classlike_name;
 
-            $storage = $this->codebase->createClassLikeStorage($fq_classlike_name);
+            if (!$storage) {
+                $storage = $this->codebase->createClassLikeStorage($fq_classlike_name);
+            }
 
             $storage->location = $class_location;
-            $storage->user_defined = !$this->codebase->register_global_functions;
-            $storage->stubbed = $this->codebase->register_global_functions;
+            $storage->user_defined = !$this->codebase->register_stub_files;
+            $storage->stubbed = $this->codebase->register_stub_files;
 
             $doc_comment = $node->getDocComment();
 
@@ -553,14 +557,14 @@ public function enterNode(PhpParser\Node $node)
                 $const_type = StatementsChecker::getSimpleType($this->codebase, $const->value, $this->aliases)
                     ?: Type::getMixed();
 
-                if ($this->codebase->register_global_functions) {
-                    $this->codebase->addStubbedConstantType($const->name->name, $const_type);
+                if ($this->codebase->register_stub_files || $this->codebase->register_autoload_files) {
+                    $this->codebase->addGlobalConstantType($const->name->name, $const_type);
                 }
 
                 $this->file_storage->constants[$const->name->name] = $const_type;
                 $this->file_storage->declaring_constants[$const->name->name] = $this->file_path;
             }
-        } elseif ($this->codebase->register_global_functions && $node instanceof PhpParser\Node\Stmt\If_) {
+        } elseif ($this->codebase->register_autoload_files && $node instanceof PhpParser\Node\Stmt\If_) {
             if ($node->cond instanceof PhpParser\Node\Expr\BooleanNot) {
                 if ($node->cond->expr instanceof PhpParser\Node\Expr\FuncCall
                     && $node->cond->expr->name instanceof PhpParser\Node\Name
@@ -689,13 +693,20 @@ private function registerFunctionLike(PhpParser\Node\FunctionLike $stmt, $fake_m
             $function_id = strtolower($cased_function_id);
 
             if (isset($this->file_storage->functions[$function_id])) {
+                if ($this->codebase->register_stub_files || $this->codebase->register_autoload_files) {
+                    $this->codebase->functions->addGlobalFunction(
+                        $function_id,
+                        $this->file_storage->functions[$function_id]
+                    );
+                }
+
                 return $this->file_storage->functions[$function_id];
             }
 
             $storage = new FunctionLikeStorage();
 
-            if ($this->codebase->register_global_functions) {
-                $this->codebase->functions->addStubbedFunction($function_id, $storage);
+            if ($this->codebase->register_stub_files || $this->codebase->register_autoload_files) {
+                $this->codebase->functions->addGlobalFunction($function_id, $storage);
             }
 
             $this->file_storage->functions[$function_id] = $storage;
@@ -716,11 +727,19 @@ private function registerFunctionLike(PhpParser\Node\FunctionLike $stmt, $fake_m
 
             $class_storage = $this->classlike_storages[count($this->classlike_storages) - 1];
 
+            $storage = null;
+
             if (isset($class_storage->methods[strtolower($stmt->name->name)])) {
-                throw new \InvalidArgumentException('Cannot re-register ' . $function_id);
+                if (!$this->codebase->register_stub_files) {
+                    throw new \InvalidArgumentException('Cannot re-register ' . $function_id);
+                }
+
+                $storage = $class_storage->methods[strtolower($stmt->name->name)];
             }
 
-            $storage = $class_storage->methods[strtolower($stmt->name->name)] = new MethodStorage();
+            if (!$storage) {
+                $storage = $class_storage->methods[strtolower($stmt->name->name)] = new MethodStorage();
+            }
 
             $class_name_parts = explode('\\', $fq_classlike_name);
             $class_name = array_pop($class_name_parts);
@@ -786,6 +805,7 @@ private function registerFunctionLike(PhpParser\Node\FunctionLike $stmt, $fake_m
         $has_optional_param = false;
 
         $existing_params = [];
+        $storage->params = [];
 
         /** @var PhpParser\Node\Param $param */
         foreach ($stmt->getParams() as $param) {
diff --git a/src/psalm.php b/src/psalm.php
index 65ee32a9056..b4f5e818871 100644
--- a/src/psalm.php
+++ b/src/psalm.php
@@ -315,6 +315,8 @@ function ($arg) {
     exit;
 }
 
+$debug = array_key_exists('debug', $options) || array_key_exists('debug-by-line', $options);
+
 $project_checker = new ProjectChecker(
     $config,
     new Psalm\Provider\FileProvider(),
@@ -325,12 +327,12 @@ function ($arg) {
     $show_info,
     $output_format,
     $threads,
-    array_key_exists('debug', $options) || array_key_exists('debug-by-line', $options),
+    $debug,
     isset($options['report']) && is_string($options['report']) ? $options['report'] : null,
     !isset($options['show-snippet']) || $options['show-snippet'] !== "false"
 );
 
-$config->visitComposerAutoloadFiles($project_checker);
+$config->visitComposerAutoloadFiles($project_checker, $debug);
 
 if (array_key_exists('debug-by-line', $options)) {
     $project_checker->debug_lines = true;
diff --git a/tests/ArrayAccessTest.php b/tests/ArrayAccessTest.php
index fdbaaff50d3..c114468344c 100644
--- a/tests/ArrayAccessTest.php
+++ b/tests/ArrayAccessTest.php
@@ -141,6 +141,14 @@ function takesInt(int $i) : void {}
                     $doc->loadXML("<node key=\"value\"/>");
                     $doc->getElementsByTagName("node")[0];'
             ],
+            'getOnArrayAcccess' => [
+                '<?php
+                    function foo(ArrayAccess $a) : void {
+                        echo $a[0];
+                    }',
+                'assertions' => [],
+                'error_levels' => ['MixedArgument'],
+            ],
         ];
     }
 
diff --git a/tests/ConfigTest.php b/tests/ConfigTest.php
index 71d2fec44c9..9869910b008 100644
--- a/tests/ConfigTest.php
+++ b/tests/ConfigTest.php
@@ -386,361 +386,6 @@ public function testImpossibleIssue()
         );
     }
 
-    /**
-     * @expectedException        \Psalm\Exception\ConfigException
-     * @expectedExceptionMessage Cannot resolve stubfile path
-     *
-     * @return                   void
-     */
-    public function testNonexistentStubFile()
-    {
-        $this->project_checker = $this->getProjectCheckerWithConfig(
-            Config::loadFromXML(
-                dirname(__DIR__),
-                '<?xml version="1.0"?>
-                <psalm>
-                    <projectFiles>
-                        <directory name="src" />
-                    </projectFiles>
-
-                    <stubs>
-                        <file name="stubs/invalidfile.php" />
-                    </stubs>
-                </psalm>'
-            )
-        );
-    }
-
-    /**
-     * @return void
-     */
-    public function testStubFile()
-    {
-        $this->project_checker = $this->getProjectCheckerWithConfig(
-            TestConfig::loadFromXML(
-                dirname(__DIR__),
-                '<?xml version="1.0"?>
-                <psalm>
-                    <projectFiles>
-                        <directory name="src" />
-                    </projectFiles>
-
-                    <stubs>
-                        <file name="tests/stubs/systemclass.php" />
-                    </stubs>
-                </psalm>'
-            )
-        );
-
-        $file_path = getcwd() . '/src/somefile.php';
-
-        $this->addFile(
-            $file_path,
-            '<?php
-                $a = new SystemClass();
-                echo SystemClass::HELLO;
-
-                $b = $a->foo(5, "hello");
-                $c = SystemClass::bar(5, "hello");'
-        );
-
-        $this->analyzeFile($file_path, new Context());
-    }
-
-    /**
-     * @return void
-     */
-    public function testNamespacedStubClass()
-    {
-        $this->project_checker = $this->getProjectCheckerWithConfig(
-            TestConfig::loadFromXML(
-                dirname(__DIR__),
-                '<?xml version="1.0"?>
-                <psalm>
-                    <projectFiles>
-                        <directory name="src" />
-                    </projectFiles>
-
-                    <stubs>
-                        <file name="tests/stubs/namespaced_class.php" />
-                    </stubs>
-                </psalm>'
-            )
-        );
-
-        $file_path = getcwd() . '/src/somefile.php';
-
-        $this->addFile(
-            $file_path,
-            '<?php
-                $a = new Foo\SystemClass();
-                echo Foo\SystemClass::HELLO;
-
-                $b = $a->foo(5, "hello");
-                $c = Foo\SystemClass::bar(5, "hello");'
-        );
-
-        $this->analyzeFile($file_path, new Context());
-    }
-
-    /**
-     * @return void
-     */
-    public function testStubFunction()
-    {
-        $this->project_checker = $this->getProjectCheckerWithConfig(
-            TestConfig::loadFromXML(
-                dirname(__DIR__),
-                '<?xml version="1.0"?>
-                <psalm>
-                    <projectFiles>
-                        <directory name="src" />
-                    </projectFiles>
-
-                    <stubs>
-                        <file name="tests/stubs/custom_functions.php" />
-                    </stubs>
-                </psalm>'
-            )
-        );
-
-        $file_path = getcwd() . '/src/somefile.php';
-
-        $this->addFile(
-            $file_path,
-            '<?php
-                echo barBar("hello");'
-        );
-
-        $this->analyzeFile($file_path, new Context());
-    }
-
-    /**
-     * @return void
-     */
-    public function testPolyfilledFunction()
-    {
-        $this->project_checker = $this->getProjectCheckerWithConfig(
-            TestConfig::loadFromXML(
-                dirname(__DIR__),
-                '<?xml version="1.0"?>
-                <psalm>
-                    <projectFiles>
-                        <directory name="src" />
-                    </projectFiles>
-
-                    <stubs>
-                        <file name="tests/stubs/polyfill.php" />
-                    </stubs>
-                </psalm>'
-            )
-        );
-
-        $file_path = getcwd() . '/src/somefile.php';
-
-        $this->addFile(
-            $file_path,
-            '<?php
-                $a = random_bytes(16);'
-        );
-
-        $this->analyzeFile($file_path, new Context());
-    }
-
-    /**
-     * @return void
-     */
-    public function testStubFunctionWithFunctionExists()
-    {
-        $this->project_checker = $this->getProjectCheckerWithConfig(
-            TestConfig::loadFromXML(
-                dirname(__DIR__),
-                '<?xml version="1.0"?>
-                <psalm>
-                    <projectFiles>
-                        <directory name="src" />
-                    </projectFiles>
-
-                    <stubs>
-                        <file name="tests/stubs/custom_functions.php" />
-                    </stubs>
-                </psalm>'
-            )
-        );
-
-        $file_path = getcwd() . '/src/somefile.php';
-
-        $this->addFile(
-            $file_path,
-            '<?php
-                function_exists("fooBar");
-                echo barBar("hello");'
-        );
-
-        $this->analyzeFile($file_path, new Context());
-    }
-
-    /**
-     * @return void
-     */
-    public function testNamespacedStubFunctionWithFunctionExists()
-    {
-        $this->project_checker = $this->getProjectCheckerWithConfig(
-            TestConfig::loadFromXML(
-                dirname(__DIR__),
-                '<?xml version="1.0"?>
-                <psalm>
-                    <projectFiles>
-                        <directory name="src" />
-                    </projectFiles>
-
-                    <stubs>
-                        <file name="tests/stubs/custom_functions.php" />
-                    </stubs>
-                </psalm>'
-            )
-        );
-
-        $file_path = getcwd() . '/src/somefile.php';
-
-        $this->addFile(
-            $file_path,
-            '<?php
-                namespace A;
-                function_exists("fooBar");
-                echo barBar("hello");'
-        );
-
-        $this->analyzeFile($file_path, new Context());
-    }
-
-    /**
-     * @expectedException        \Psalm\Exception\CodeException
-     * @expectedExceptionMessage UndefinedFunction - /src/somefile.php:2 - Function barBar does not exist
-     *
-     * @return                   void
-     */
-    public function testNoStubFunction()
-    {
-        $this->project_checker = $this->getProjectCheckerWithConfig(
-            TestConfig::loadFromXML(
-                dirname(__DIR__),
-                '<?xml version="1.0"?>
-                <psalm>
-                    <projectFiles>
-                        <directory name="src" />
-                    </projectFiles>
-                </psalm>'
-            )
-        );
-
-        $file_path = getcwd() . '/src/somefile.php';
-
-        $this->addFile(
-            $file_path,
-            '<?php
-                echo barBar("hello");'
-        );
-
-        $this->analyzeFile($file_path, new Context());
-    }
-
-    /**
-     * @return void
-     */
-    public function testNamespacedStubFunction()
-    {
-        $this->project_checker = $this->getProjectCheckerWithConfig(
-            TestConfig::loadFromXML(
-                dirname(__DIR__),
-                '<?xml version="1.0"?>
-                <psalm>
-                    <projectFiles>
-                        <directory name="src" />
-                    </projectFiles>
-
-                    <stubs>
-                        <file name="tests/stubs/namespaced_functions.php" />
-                    </stubs>
-                </psalm>'
-            )
-        );
-
-        $file_path = getcwd() . '/src/somefile.php';
-
-        $this->addFile(
-            $file_path,
-            '<?php
-                echo Foo\barBar("hello");'
-        );
-
-        $this->analyzeFile($file_path, new Context());
-    }
-
-    /**
-     * @return void
-     */
-    public function testConditionalNamespacedStubFunction()
-    {
-        $this->project_checker = $this->getProjectCheckerWithConfig(
-            TestConfig::loadFromXML(
-                dirname(__DIR__),
-                '<?xml version="1.0"?>
-                <psalm>
-                    <projectFiles>
-                        <directory name="src" />
-                    </projectFiles>
-
-                    <stubs>
-                        <file name="tests/stubs/conditional_namespaced_functions.php" />
-                    </stubs>
-                </psalm>'
-            )
-        );
-
-        $file_path = getcwd() . '/src/somefile.php';
-
-        $this->addFile(
-            $file_path,
-            '<?php
-                echo Foo\barBar("hello");'
-        );
-
-        $this->analyzeFile($file_path, new Context());
-    }
-
-    /**
-     * @return void
-     */
-    public function testStubFileWithExistingClassDefinition()
-    {
-        $this->project_checker = $this->getProjectCheckerWithConfig(
-            TestConfig::loadFromXML(
-                dirname(__DIR__),
-                '<?xml version="1.0"?>
-                <psalm>
-                    <projectFiles>
-                        <directory name="src" />
-                    </projectFiles>
-
-                    <stubs>
-                        <file name="tests/stubs/logicexception.php" />
-                    </stubs>
-                </psalm>'
-            )
-        );
-
-        $file_path = getcwd() . '/src/somefile.php';
-
-        $this->addFile(
-            $file_path,
-            '<?php
-                $a = new LogicException(5);'
-        );
-
-        $this->analyzeFile($file_path, new Context());
-    }
-
     /**
      * @expectedException        \Psalm\Exception\CodeException
      * @expectedExceptionMessage MissingReturnType
diff --git a/tests/FileManipulationTest.php b/tests/FileManipulationTest.php
index c0ec92d697d..efe0cddd71b 100644
--- a/tests/FileManipulationTest.php
+++ b/tests/FileManipulationTest.php
@@ -46,10 +46,6 @@ public function testValidCode($input_code, $output_code, $php_version, array $is
 
         $config = new TestConfig();
 
-        if (empty($issues_to_fix)) {
-            $config->addPluginPath('examples/ClassUnqualifier.php');
-        }
-
         $this->project_checker = new \Psalm\Checker\ProjectChecker(
             $config,
             $this->file_provider,
@@ -58,6 +54,11 @@ public function testValidCode($input_code, $output_code, $php_version, array $is
             new \Psalm\Provider\NoCache\NoClassLikeStorageCacheProvider()
         );
 
+        if (empty($issues_to_fix)) {
+            $config->addPluginPath('examples/ClassUnqualifier.php');
+            $config->initializePlugins($this->project_checker);
+        }
+
         $context = new Context();
 
         $file_path = self::$src_dir_path . 'somefile.php';
diff --git a/tests/StubTest.php b/tests/StubTest.php
new file mode 100644
index 00000000000..df502e22ee4
--- /dev/null
+++ b/tests/StubTest.php
@@ -0,0 +1,550 @@
+<?php
+namespace Psalm\Tests;
+
+use Psalm\Checker\FileChecker;
+use Psalm\Config;
+use Psalm\Context;
+
+class StubTest extends TestCase
+{
+    /** @var TestConfig */
+    protected static $config;
+
+    /** @var \Psalm\Checker\ProjectChecker */
+    protected $project_checker;
+
+    /**
+     * @return void
+     */
+    public static function setUpBeforeClass()
+    {
+        self::$config = new TestConfig();
+
+        if (!defined('PSALM_VERSION')) {
+            define('PSALM_VERSION', '2.0.0');
+        }
+
+        if (!defined('PHP_PARSER_VERSION')) {
+            define('PHP_PARSER_VERSION', '4.0.0');
+        }
+    }
+
+    /**
+     * @return void
+     */
+    public function setUp()
+    {
+        FileChecker::clearCache();
+        $this->file_provider = new Provider\FakeFileProvider();
+    }
+
+    /**
+     * @param  Config $config
+     *
+     * @return \Psalm\Checker\ProjectChecker
+     */
+    private function getProjectCheckerWithConfig(Config $config)
+    {
+        return new \Psalm\Checker\ProjectChecker(
+            $config,
+            $this->file_provider,
+            new Provider\FakeParserCacheProvider(),
+            new \Psalm\Provider\NoCache\NoFileStorageCacheProvider(),
+            new \Psalm\Provider\NoCache\NoClassLikeStorageCacheProvider()
+        );
+    }
+
+    /**
+     * @expectedException        \Psalm\Exception\ConfigException
+     * @expectedExceptionMessage Cannot resolve stubfile path
+     *
+     * @return                   void
+     */
+    public function testNonexistentStubFile()
+    {
+        $this->project_checker = $this->getProjectCheckerWithConfig(
+            Config::loadFromXML(
+                dirname(__DIR__),
+                '<?xml version="1.0"?>
+                <psalm>
+                    <projectFiles>
+                        <directory name="src" />
+                    </projectFiles>
+
+                    <stubs>
+                        <file name="stubs/invalidfile.php" />
+                    </stubs>
+                </psalm>'
+            )
+        );
+    }
+
+    /**
+     * @return void
+     */
+    public function testStubFile()
+    {
+        $this->project_checker = $this->getProjectCheckerWithConfig(
+            TestConfig::loadFromXML(
+                dirname(__DIR__),
+                '<?xml version="1.0"?>
+                <psalm>
+                    <projectFiles>
+                        <directory name="src" />
+                    </projectFiles>
+
+                    <stubs>
+                        <file name="tests/stubs/systemclass.php" />
+                    </stubs>
+                </psalm>'
+            )
+        );
+
+        $file_path = getcwd() . '/src/somefile.php';
+
+        $this->addFile(
+            $file_path,
+            '<?php
+                $a = new SystemClass();
+                echo SystemClass::HELLO;
+
+                $b = $a->foo(5, "hello");
+                $c = SystemClass::bar(5, "hello");'
+        );
+
+        $this->analyzeFile($file_path, new Context());
+    }
+
+    /**
+     * @return void
+     */
+    public function testNamespacedStubClass()
+    {
+        $this->project_checker = $this->getProjectCheckerWithConfig(
+            TestConfig::loadFromXML(
+                dirname(__DIR__),
+                '<?xml version="1.0"?>
+                <psalm>
+                    <projectFiles>
+                        <directory name="src" />
+                    </projectFiles>
+
+                    <stubs>
+                        <file name="tests/stubs/namespaced_class.php" />
+                    </stubs>
+                </psalm>'
+            )
+        );
+
+        $file_path = getcwd() . '/src/somefile.php';
+
+        $this->addFile(
+            $file_path,
+            '<?php
+                $a = new Foo\SystemClass();
+                echo Foo\SystemClass::HELLO;
+
+                $b = $a->foo(5, "hello");
+                $c = Foo\SystemClass::bar(5, "hello");'
+        );
+
+        $this->analyzeFile($file_path, new Context());
+    }
+
+    /**
+     * @return void
+     */
+    public function testStubFunction()
+    {
+        $this->project_checker = $this->getProjectCheckerWithConfig(
+            TestConfig::loadFromXML(
+                dirname(__DIR__),
+                '<?xml version="1.0"?>
+                <psalm>
+                    <projectFiles>
+                        <directory name="src" />
+                    </projectFiles>
+
+                    <stubs>
+                        <file name="tests/stubs/custom_functions.php" />
+                    </stubs>
+                </psalm>'
+            )
+        );
+
+        $file_path = getcwd() . '/src/somefile.php';
+
+        $this->addFile(
+            $file_path,
+            '<?php
+                echo barBar("hello");'
+        );
+
+        $this->analyzeFile($file_path, new Context());
+    }
+
+    /**
+     * @return void
+     */
+    public function testPolyfilledFunction()
+    {
+        $this->project_checker = $this->getProjectCheckerWithConfig(
+            TestConfig::loadFromXML(
+                dirname(__DIR__),
+                '<?xml version="1.0"?>
+                <psalm
+                    autoloader="tests/stubs/polyfill.php"
+                >
+                    <projectFiles>
+                        <directory name="src" />
+                    </projectFiles>
+                </psalm>'
+            )
+        );
+
+        $file_path = getcwd() . '/src/somefile.php';
+
+        $this->addFile(
+            $file_path,
+            '<?php
+                $a = random_bytes(16);'
+        );
+
+        $this->analyzeFile($file_path, new Context());
+    }
+
+    /**
+     * @return void
+     */
+    public function testStubFunctionWithFunctionExists()
+    {
+        $this->project_checker = $this->getProjectCheckerWithConfig(
+            TestConfig::loadFromXML(
+                dirname(__DIR__),
+                '<?xml version="1.0"?>
+                <psalm>
+                    <projectFiles>
+                        <directory name="src" />
+                    </projectFiles>
+
+                    <stubs>
+                        <file name="tests/stubs/custom_functions.php" />
+                    </stubs>
+                </psalm>'
+            )
+        );
+
+        $file_path = getcwd() . '/src/somefile.php';
+
+        $this->addFile(
+            $file_path,
+            '<?php
+                function_exists("fooBar");
+                echo barBar("hello");'
+        );
+
+        $this->analyzeFile($file_path, new Context());
+    }
+
+    /**
+     * @return void
+     */
+    public function testNamespacedStubFunctionWithFunctionExists()
+    {
+        $this->project_checker = $this->getProjectCheckerWithConfig(
+            TestConfig::loadFromXML(
+                dirname(__DIR__),
+                '<?xml version="1.0"?>
+                <psalm>
+                    <projectFiles>
+                        <directory name="src" />
+                    </projectFiles>
+
+                    <stubs>
+                        <file name="tests/stubs/custom_functions.php" />
+                    </stubs>
+                </psalm>'
+            )
+        );
+
+        $file_path = getcwd() . '/src/somefile.php';
+
+        $this->addFile(
+            $file_path,
+            '<?php
+                namespace A;
+                function_exists("fooBar");
+                echo barBar("hello");'
+        );
+
+        $this->analyzeFile($file_path, new Context());
+    }
+
+    /**
+     * @expectedException        \Psalm\Exception\CodeException
+     * @expectedExceptionMessage UndefinedFunction - /src/somefile.php:2 - Function barBar does not exist
+     *
+     * @return                   void
+     */
+    public function testNoStubFunction()
+    {
+        $this->project_checker = $this->getProjectCheckerWithConfig(
+            TestConfig::loadFromXML(
+                dirname(__DIR__),
+                '<?xml version="1.0"?>
+                <psalm>
+                    <projectFiles>
+                        <directory name="src" />
+                    </projectFiles>
+                </psalm>'
+            )
+        );
+
+        $file_path = getcwd() . '/src/somefile.php';
+
+        $this->addFile(
+            $file_path,
+            '<?php
+                echo barBar("hello");'
+        );
+
+        $this->analyzeFile($file_path, new Context());
+    }
+
+    /**
+     * @return void
+     */
+    public function testNamespacedStubFunction()
+    {
+        $this->project_checker = $this->getProjectCheckerWithConfig(
+            TestConfig::loadFromXML(
+                dirname(__DIR__),
+                '<?xml version="1.0"?>
+                <psalm>
+                    <projectFiles>
+                        <directory name="src" />
+                    </projectFiles>
+
+                    <stubs>
+                        <file name="tests/stubs/namespaced_functions.php" />
+                    </stubs>
+                </psalm>'
+            )
+        );
+
+        $file_path = getcwd() . '/src/somefile.php';
+
+        $this->addFile(
+            $file_path,
+            '<?php
+                echo Foo\barBar("hello");'
+        );
+
+        $this->analyzeFile($file_path, new Context());
+    }
+
+    /**
+     * @return void
+     */
+    public function testConditionalNamespacedStubFunction()
+    {
+        $this->project_checker = $this->getProjectCheckerWithConfig(
+            TestConfig::loadFromXML(
+                dirname(__DIR__),
+                '<?xml version="1.0"?>
+                <psalm>
+                    <projectFiles>
+                        <directory name="src" />
+                    </projectFiles>
+
+                    <stubs>
+                        <file name="tests/stubs/conditional_namespaced_functions.php" />
+                    </stubs>
+                </psalm>'
+            )
+        );
+
+        $file_path = getcwd() . '/src/somefile.php';
+
+        $this->addFile(
+            $file_path,
+            '<?php
+                echo Foo\barBar("hello");'
+        );
+
+        $this->analyzeFile($file_path, new Context());
+    }
+
+    /**
+     * @return void
+     */
+    public function testStubFileWithExistingClassDefinition()
+    {
+        $this->project_checker = $this->getProjectCheckerWithConfig(
+            TestConfig::loadFromXML(
+                dirname(__DIR__),
+                '<?xml version="1.0"?>
+                <psalm>
+                    <projectFiles>
+                        <directory name="src" />
+                    </projectFiles>
+
+                    <stubs>
+                        <file name="tests/stubs/logicexception.php" />
+                    </stubs>
+                </psalm>'
+            )
+        );
+
+        $file_path = getcwd() . '/src/somefile.php';
+
+        $this->addFile(
+            $file_path,
+            '<?php
+                $a = new LogicException(5);'
+        );
+
+        $this->analyzeFile($file_path, new Context());
+    }
+
+    /**
+     * @return void
+     */
+    public function testStubFileWithPartialClassDefinitionWithMoreMethods()
+    {
+        $this->project_checker = $this->getProjectCheckerWithConfig(
+            TestConfig::loadFromXML(
+                dirname(__DIR__),
+                '<?xml version="1.0"?>
+                <psalm>
+                    <projectFiles>
+                        <directory name="src" />
+                    </projectFiles>
+
+                    <stubs>
+                        <file name="tests/stubs/partial_class.php" />
+                    </stubs>
+                </psalm>'
+            )
+        );
+
+        $file_path = getcwd() . '/src/somefile.php';
+
+        $this->addFile(
+            $file_path,
+            '<?php
+                namespace Foo;
+
+                class PartiallyStubbedClass  {
+                    /**
+                     * @param string $a
+                     * @return object
+                     */
+                    public function foo(string $a) {
+                        return new self;
+                    }
+
+                    public function bar(int $i) : void {}
+                }
+
+                class A {}
+
+                (new PartiallyStubbedClass())->foo(A::class);
+                (new PartiallyStubbedClass())->bar(5);'
+        );
+
+        $this->analyzeFile($file_path, new Context());
+    }
+
+    /**
+     * @expectedException        \Psalm\Exception\CodeException
+     * @expectedExceptionMessage TypeCoercion
+     *
+     * @return                   void
+     */
+    public function testStubFileWithPartialClassDefinitionWithCoercion()
+    {
+        $this->project_checker = $this->getProjectCheckerWithConfig(
+            TestConfig::loadFromXML(
+                dirname(__DIR__),
+                '<?xml version="1.0"?>
+                <psalm>
+                    <projectFiles>
+                        <directory name="src" />
+                    </projectFiles>
+
+                    <stubs>
+                        <file name="tests/stubs/partial_class.php" />
+                    </stubs>
+                </psalm>'
+            )
+        );
+
+        $file_path = getcwd() . '/src/somefile.php';
+
+        $this->addFile(
+            $file_path,
+            '<?php
+                namespace Foo;
+
+                class PartiallyStubbedClass  {
+                    /**
+                     * @param string $a
+                     * @return object
+                     */
+                    public function foo(string $a) {
+                        return new self;
+                    }
+                }
+
+                (new PartiallyStubbedClass())->foo("dasda");'
+        );
+
+        $this->analyzeFile($file_path, new Context());
+    }
+
+    /**
+     * @expectedException        \Psalm\Exception\CodeException
+     * @expectedExceptionMessage InvalidReturnStatement
+     *
+     * @return                   void
+     */
+    public function testStubFileWithPartialClassDefinitionGeneralReturnType()
+    {
+        $this->project_checker = $this->getProjectCheckerWithConfig(
+            TestConfig::loadFromXML(
+                dirname(__DIR__),
+                '<?xml version="1.0"?>
+                <psalm>
+                    <projectFiles>
+                        <directory name="src" />
+                    </projectFiles>
+
+                    <stubs>
+                        <file name="tests/stubs/partial_class.php" />
+                    </stubs>
+                </psalm>'
+            )
+        );
+
+        $file_path = getcwd() . '/src/somefile.php';
+
+        $this->addFile(
+            $file_path,
+            '<?php
+                namespace Foo;
+
+                class PartiallyStubbedClass  {
+                    /**
+                     * @param string $a
+                     * @return object
+                     */
+                    public function foo(string $a) {
+                        return new \stdClass;
+                    }
+                }'
+        );
+
+        $this->analyzeFile($file_path, new Context());
+    }
+}
diff --git a/tests/TestCase.php b/tests/TestCase.php
index c020886bb46..986ec2adc07 100644
--- a/tests/TestCase.php
+++ b/tests/TestCase.php
@@ -90,6 +90,8 @@ public function analyzeFile($file_path, \Psalm\Context $context)
 
         $codebase->scanFiles();
 
+        $codebase->config->visitStubFiles($codebase);
+
         $file_checker = new FileChecker(
             $this->project_checker,
             $file_path,
diff --git a/tests/stubs/partial_class.php b/tests/stubs/partial_class.php
new file mode 100644
index 00000000000..16049b67dd6
--- /dev/null
+++ b/tests/stubs/partial_class.php
@@ -0,0 +1,11 @@
+<?php
+
+namespace Foo;
+
+class PartiallyStubbedClass  {
+    /**
+     * @param class-string    $a
+     * @return PartiallyStubbedClass
+     */
+    public function foo($a) {}
+}