diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
index dbaab727c4..3b97354c8a 100644
--- a/CODE_OF_CONDUCT.md
+++ b/CODE_OF_CONDUCT.md
@@ -40,7 +40,7 @@ Project maintainers who do not follow or enforce the Code of Conduct in good fai
 
 ## Attribution
 
-This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [https://www.contributor-covenant.org/version/1/4/code-of-conduct/][version]
 
-[homepage]: http://contributor-covenant.org
-[version]: http://contributor-covenant.org/version/1/4/
+[homepage]: https://www.contributor-covenant.org/
+[version]: https://www.contributor-covenant.org/version/1/4/code-of-conduct/
diff --git a/README.rst b/README.rst
index df1242f3d0..6b703c2cc3 100644
--- a/README.rst
+++ b/README.rst
@@ -40,7 +40,7 @@ If you prefer to follow the git repository, the following branch and tag names m
 
 * ``STABLE`` is the current stable release.
 * ``master`` is the development branch.
-* Releases are tagged, for example version 4.0.1 was tagged as ``RELEASE_4_0_1``.
+* Releases are tagged, for example version 5.0.1 was tagged as ``RELEASE_5_0_1``.
 
 Note that phpMyAdmin uses Composer to manage library dependencies, when using git
 development versions you must manually run Composer.
diff --git a/doc/config.rst b/doc/config.rst
index 7525989d9e..d723e9c2fc 100644
--- a/doc/config.rst
+++ b/doc/config.rst
@@ -20,7 +20,7 @@ the file. This file is for over-writing the defaults; if you wish to use the
 default value there's no need to add a line here.
 
 The parameters which relate to design (like colors) are placed in
-:file:`themes/themename/layout.inc.php`. You might also want to create
+:file:`themes/themename/scss/_variables.scss`. You might also want to create
 :file:`config.footer.inc.php` and :file:`config.header.inc.php` files to add
 your site specific code to be included on start and end of each page.
 
@@ -217,8 +217,8 @@ Basic settings
 
     Setting this to ``true`` allows phpMyAdmin to be included inside a frame,
     and is a potential security hole allowing cross-frame scripting attacks or
-    clickjacking. Setting this to 'sameorigin' prevents phpMyAdmin to be 
-    included from another document in a frame, unless that document belongs 
+    clickjacking. Setting this to 'sameorigin' prevents phpMyAdmin to be
+    included from another document in a frame, unless that document belongs
     to the same domain.
 
 Server connection settings
@@ -2795,7 +2795,7 @@ Web server settings
 Theme settings
 --------------
 
-    Please directly modify :file:`themes/themename/layout.inc.php`, although
+    Please directly modify :file:`themes/themename/scss/_variables.scss`, although
     your changes will be overwritten with the next update.
 
 Design customization
diff --git a/doc/themes.rst b/doc/themes.rst
index 1f22521b68..23cdb4fc67 100644
--- a/doc/themes.rst
+++ b/doc/themes.rst
@@ -27,7 +27,7 @@ To create a theme:
 * copy the files and directories from ``pmahomme`` to "your\_theme\_name"
 * edit the css-files in "your\_theme\_name/css"
 * put your new images in "your\_theme\_name/img"
-* edit :file:`layout.inc.php` in "your\_theme\_name"
+* edit :file:`_variables.scss` in "your\_theme\_name/scss"
 * edit :file:`theme.json` in "your\_theme\_name" to contain theme metadata (see below)
 * make a new screenshot of your theme and save it under
   "your\_theme\_name/screen.png"
diff --git a/libraries/classes/Config/Validator.php b/libraries/classes/Config/Validator.php
index d010439bd4..41ce4bdaf6 100644
--- a/libraries/classes/Config/Validator.php
+++ b/libraries/classes/Config/Validator.php
@@ -42,8 +42,7 @@ use function trim;
  * Validation class for various validation functions
  *
  * Validation function takes two argument: id for which it is called
- * and array of fields' values (usually values for entire formset, as defined
- * in forms.inc.php).
+ * and array of fields' values (usually values for entire formset).
  * The function must always return an array with an error (or error array)
  * assigned to a form element (formset name or field path). Even if there are
  * no errors, key must be set with an empty value.
diff --git a/libraries/classes/Plugins/Export/README b/libraries/classes/Plugins/Export/README.md
similarity index 99%
rename from libraries/classes/Plugins/Export/README
rename to libraries/classes/Plugins/Export/README.md
index 3b11c63f37..c9e479d4c3 100644
--- a/libraries/classes/Plugins/Export/README
+++ b/libraries/classes/Plugins/Export/README.md
@@ -1,8 +1,11 @@
+# Export plugin creation
+
 This directory holds export plugins for phpMyAdmin. Any new plugin should
 basically follow the structure presented here. Official plugins need to
 have str* messages with their definition in language files, but if you build
 some plugins for your use, you can directly use texts in plugin.
 
+```php
 <?php
 /**
  * [Name] export plugin for phpMyAdmin
@@ -191,7 +194,7 @@ class Export[Name] extends PhpMyAdmin\Plugins\ExportPlugin
         return true;
     }
 
-    // optional - implement other methods defined in PhpMyAdmin\Plugins\ExportPlugin.class.php:
+    // optional - implement other methods defined in PhpMyAdmin\Plugins\ExportPlugin.php:
     //  - exportRoutines()
     //  - exportStructure()
     //  - getTableDefStandIn()
@@ -251,4 +254,4 @@ class Export[Name] extends PhpMyAdmin\Plugins\ExportPlugin
         $this->_globalVariableName = $global_variable_name;
     }
 }
-?>
+```
diff --git a/libraries/classes/Plugins/Import/README b/libraries/classes/Plugins/Import/README.md
similarity index 99%
rename from libraries/classes/Plugins/Import/README
rename to libraries/classes/Plugins/Import/README.md
index d39c85650e..41d27ec07e 100644
--- a/libraries/classes/Plugins/Import/README
+++ b/libraries/classes/Plugins/Import/README.md
@@ -1,7 +1,10 @@
+# Import plugin creation
+
 This directory holds import plugins for phpMyAdmin. Any new plugin should
 basically follow the structure presented here. The messages must use our
 gettext mechanism, see https://wiki.phpmyadmin.net/pma/Gettext_for_developers.
 
+```php
 <?php
 /**
  * [Name] import plugin for phpMyAdmin
@@ -152,4 +155,4 @@ class Import[Name] extends ImportPlugin
         $this->_myOptionalVariable = $my_optional_variable;
     }
 }
-?>
+```
diff --git a/libraries/classes/Plugins/Transformations/TEMPLATE b/libraries/classes/Plugins/Transformations/TEMPLATE
index 7d2b2ff728..9a83715d55 100644
--- a/libraries/classes/Plugins/Transformations/TEMPLATE
+++ b/libraries/classes/Plugins/Transformations/TEMPLATE
@@ -1,5 +1,4 @@
 <?php
-// vim: expandtab sw=4 ts=4 sts=4:
 /**
  * This file contains the basic structure for a specific MIME Type and Subtype
  * transformations class.
@@ -29,7 +28,7 @@ class [MIMEType][MIMESubtype][TransformationName]
      */
     public static function getMIMEType()
     {
-        return "[MIMEType]";
+        return '[MIMEType]';
     }
 
     /**
@@ -39,7 +38,7 @@ class [MIMEType][MIMESubtype][TransformationName]
      */
     public static function getMIMESubtype()
     {
-        return "[MIMESubtype]";
+        return '[MIMESubtype]';
     }
 }
 ?>
diff --git a/libraries/classes/Plugins/Transformations/TEMPLATE_ABSTRACT b/libraries/classes/Plugins/Transformations/TEMPLATE_ABSTRACT
index 4087ac9e2b..261356a4c7 100644
--- a/libraries/classes/Plugins/Transformations/TEMPLATE_ABSTRACT
+++ b/libraries/classes/Plugins/Transformations/TEMPLATE_ABSTRACT
@@ -1,5 +1,4 @@
 <?php
-// vim: expandtab sw=4 ts=4 sts=4:
 /**
  * This file contains the basic structure for an abstract class defining a
  * transformation.
@@ -67,7 +66,7 @@ abstract class [TransformationName]TransformationsPlugin
      */
     public static function getName()
     {
-        return "[TransformationName]";
+        return '[TransformationName]';
     }
 }
 ?>
diff --git a/libraries/config.default.php b/libraries/config.default.php
index 07db8b89a8..a509f4ca95 100644
--- a/libraries/config.default.php
+++ b/libraries/config.default.php
@@ -2400,13 +2400,11 @@ $cfg['AvailableCharsets'] = [
 /*******************************************************************************
  * Customization & design
  *
- * The graphical settings are now located in themes/theme-name/layout.inc.php
+ * The graphical settings are now located in themes/theme-name/scss/_variables.scss
  */
 
 /**
  * enable the left panel pointer
- * see also LeftPointerColor
- * in layout.inc.php
  *
  * @global boolean $cfg['NavigationTreePointerEnable']
  */
@@ -2414,8 +2412,6 @@ $cfg['NavigationTreePointerEnable'] = true;
 
 /**
  * enable the browse pointer
- * see also BrowsePointerColor
- * in layout.inc.php
  *
  * @global boolean $cfg['BrowsePointerEnable']
  */
@@ -2423,8 +2419,6 @@ $cfg['BrowsePointerEnable'] = true;
 
 /**
  * enable the browse marker
- * see also BrowseMarkerColor
- * in layout.inc.php
  *
  * @global boolean $cfg['BrowseMarkerEnable']
  */