Use realpath for excluding and including individual files

This commit makes sure that paths persisted in internal structure are
always represented by the real path not relative no matter how they were
discovered. This fixes issue with being unable to exclude file loaded
via directories configuration or vice versa.

src/Extension.php

@@ -34,6 +34,7 @@
 
 use function sprintf;
 use function sys_get_temp_dir;
+use function realpath;
 
 class Extension implements ExtensionInterface
 {
@@ -218,7 +219,7 @@ public function initCodeCoverage(Filter $filter, array $filterConfig, ?bool $bra
 
         foreach ($filterConfig['include']['directories'] as $directoryToInclude => $details) {
             foreach ((new FileIteratorFacade())->getFilesAsArray($directoryToInclude, $details['suffix'], $details['prefix']) as $fileToInclude) {
-                $files[$fileToInclude] = $fileToInclude;
+                $files[realpath($fileToInclude)] = realpath($fileToInclude);
             }
         }
 
@@ -233,7 +234,7 @@ public function initCodeCoverage(Filter $filter, array $filterConfig, ?bool $bra
         }
 
         foreach ($filterConfig['exclude']['files'] as $fileToExclude) {
-            unset($files[$fileToExclude]);
+            unset($files[realpath($fileToExclude)]);
         }
 
         foreach ($files as $file) {