[TASK] Overwrite run command (#1054)

Other than what we did before we do now a full overwrite of the run
command. This allows us to remove a number of less optimal constructions
in the command. The change itself is empowered by the changes in
phpdocumentor/guides-cli 1.9 which now provides a number of helper
classes to simplify self build run commands.

Author: jaapio

composer.json

@@ -9,12 +9,12 @@
         "ext-libxml": "*",
         "brotkrueml/twig-codehighlight": "^1.0",
         "league/flysystem": "^1.1.10",
-        "phpdocumentor/filesystem": "^1.7",
-        "phpdocumentor/guides": "^1.7",
-        "phpdocumentor/guides-cli": "^1.8.1",
+        "phpdocumentor/filesystem": "^1.9",
+        "phpdocumentor/guides": "^1.9",
+        "phpdocumentor/guides-cli": "^1.9",
         "phpdocumentor/guides-graphs": "^1.0",
-        "phpdocumentor/guides-markdown": "^1.7",
-        "phpdocumentor/guides-restructured-text": "^1.7",
+        "phpdocumentor/guides-markdown": "^1.9",
+        "phpdocumentor/guides-restructured-text": "^1.9",
         "phpdocumentor/guides-theme-bootstrap": "^1.7",
         "phpdocumentor/guides-theme-rst": "^1.7",
         "symfony/clock": "^6.4",