Update the nix-shell environment (#13316)

* Nix: Allow calls to `bin/qmk` even when the build was started by `qmk`

The `$PATH` modifications performed by the Nix wrapper for the `qmk`
executable prevent `bin/qmk` from working properly (the changed `$PATH`
contains a wrong `python3` executable which does not have the needed
Python modules in its module path).  As a workaround, disable the
generation of that wrapper for the `qmk` Python package (there is yet
another wrapper generated while building the Python environment, which
would still set the Python module path properly when running `qmk`).

Although `bin/qmk` is officially deprecated, QMK CLI still invokes it in
some cases (at least `qmk doctor` and `qmk pytest`), therefore keeping
these invocations working is useful.

* Nix: Update `util/nix/pyproject.toml` to match `requirements*.txt`

Update the Python dependency information used by Poetry to match the
current state of the qmk_firmware code.

* Nix: Bump QMK CLI dependency to 1.0.0; bump other Python deps

Update Python dependencies for nix-shell to the most recent releases:

 - dotty-dict: 1.3.0 -> no longer used
 - milc: 1.4.2 -> 1.6.2
 - pep8-naming: 0.11.1 -> 0.12.1
 - pygments: 2.9.0 -> 2.10.0
 - pyrsistent: 0.17.3 -> 0.18.0
 - pyusb: 1.1.1 -> 1.2.1
 - setuptools-scm: 6.0.1 -> no longer used
 - qmk: 0.1.0 -> 1.0.0
 - qmk-dotty-dict: not used -> 1.3.0.post1
 - yapf: 0.30.0 -> 0.31.0

Note to self: The command to update Python dependencies changed to:

    ( cd util/nix && nix run 'nixpkgs#poetry' -- update --lock )

shell.nix

@@ -12,6 +12,13 @@ let
   # files if the requirements*.txt files change
   pythonEnv = poetry2nix.mkPoetryEnv {
     projectDir = ./util/nix;
+    overrides = poetry2nix.overrides.withDefaults (self: super: {
+      qmk = super.qmk.overridePythonAttrs(old: {
+        # Allow QMK CLI to run "bin/qmk" as a subprocess (the wrapper changes
+        # $PATH and breaks these invocations).
+        dontWrapPythonPrograms = true;
+      });
+    });
   };
 in