treewide: avoid passing pkgs to our lib

In the two places where our "helpers" lib is exclusively internal
(flake module args and building the docs), we no longer supply `pkgs`.

In the other 4 locations, we now note why we still do in a comment.

lib/tests.nix

@@ -45,6 +45,7 @@ let
     }@args:
     let
       helpers = import ../lib {
+        # NOTE: must match the user-facing functions, so we still include the `pkgs` argument
         inherit pkgs lib;
         # TODO: deprecate helpers.enableExceptInTests,
         # add a context option e.g. `config.isTest`?