pip: Update system packages based on fdsdk 25.08

Author: bbhtt

pip/flatpak-pip-generator.py

@@ -548,14 +548,12 @@ def get_flatpak_runtime_scope(runtime: str) -> str:
 # Python3 packages that come as part of org.freedesktop.Sdk.
 system_packages = [
     "cython",
-    "easy_install",
     "mako",
     "markdown",
     "meson",
+    "packaging",
     "pip",
-    "pygments",
     "setuptools",
-    "six",
     "wheel",
 ]