Fix composability of python package overriding

As discussed at NixOS/nixpkgs#44426, `packageOverrides` is not
composable. Haskell packaging has (had?) a similar problem.

The solution, which works fairly elegantly, is to instead use
`python3.pkgs.overrideScope` to define a new set of `pkgs`, and replace
the original `python3.pkgs` with that.

Importantly, the arguments to `packageOverrides` do not need to change,
to be used with `overrideScope`.

Note, also, that `python3.pkgs.overrideScope` corresponds to
`lib.overrideScope'` (with the prime).

dependencies/python/default.nix

@@ -12,10 +12,10 @@ let
 in
 {
   overlays.python = final: prev: {
-    python3 = prev.python3.override {
-      packageOverrides = lib.composeManyExtensions [
+    python3 = prev.python3 // {
+      pkgs = prev.python3.pkgs.overrideScope (lib.composeManyExtensions [
         (_: _: newPackages final prev)
-      ];
+      ]);
     };
 
     python3Packages = final.python3.pkgs;