Prevent unnecessary warnings

src/Psalm/Internal/Analyzer/ClassAnalyzer.php

@@ -1746,6 +1746,7 @@ class ClassAnalyzer extends ClassLikeAnalyzer
                                     && ($local_offset
                                         = array_search($t->param_name, array_keys($storage->template_types)))
                                         !== false
+                                    && isset($storage->template_covariants[$local_offset])
                                     && $storage->template_covariants[$local_offset]
                                 ) {
                                     if (IssueBuffer::accepts(

src/Psalm/Internal/Codebase/Analyzer.php

@@ -247,6 +247,13 @@ class Analyzer
             $project_analyzer->interpretRefactors();
         }
 
+        $this->files_to_analyze = array_filter(
+            $this->files_to_analyze,
+            function (string $file_path) : bool {
+                return $this->file_provider->fileExists($file_path);
+            }
+        );
+
         $analysis_worker =
             /**
              * @param int $_

src/Psalm/Internal/Codebase/Scanner.php

@@ -358,8 +358,9 @@ class Scanner
         $files_to_scan = array_filter(
             $this->files_to_scan,
             function (string $file_path) : bool {
-                return !isset($this->scanned_files[$file_path])
+                return $this->file_provider->fileExists($file_path)
-                    || (isset($this->files_to_deep_scan[$file_path]) && !$this->scanned_files[$file_path]);
+                    && (!isset($this->scanned_files[$file_path])
+                        || (isset($this->files_to_deep_scan[$file_path]) && !$this->scanned_files[$file_path]));
             }
         );
 

src/Psalm/Internal/Provider/FileProvider.php

@@ -35,6 +35,10 @@ class FileProvider
             return $this->open_files[strtolower($file_path)];
         }
 
+        if (!file_exists($file_path)) {
+            throw new \UnexpectedValueException('File ' . $file_path . ' should exist to get contents');
+        }
+
         return (string)file_get_contents($file_path);
     }
 
@@ -77,6 +81,10 @@ class FileProvider
      */
     public function getModifiedTime($file_path)
     {
+        if (!file_exists($file_path)) {
+            throw new \UnexpectedValueException('File should exist to get modified time');
+        }
+
         return (int)filemtime($file_path);
     }
 

src/Psalm/Internal/Provider/FileReferenceCacheProvider.php

@@ -649,8 +649,8 @@ class FileReferenceCacheProvider
         $cache_directory = Config::getInstance()->getCacheDirectory();
 
         if ($cache_directory) {
-            if (file_exists($cache_directory)) {
+            if (!file_exists($cache_directory)) {
-                mkdir($cache_directory, 0777, true);
+                \mkdir($cache_directory, 0777, true);
             }
 
             $config_hash_cache_location = $cache_directory . DIRECTORY_SEPARATOR . self::CONFIG_HASH_CACHE_NAME;