treewide: migrate packages to pkgs/by-name, take 1

We are migrating packages that meet below requirements:

1. using `callPackage`
2. called path is a directory
3. overriding set is empty (`{ }`)
4. not containing path expressions other than relative path (to
makenixpkgs-vet happy)
5. not referenced by nix files outside of the directory, other
than`pkgs/top-level/all-packages.nix`
6. not referencing nix files outside of the directory
7. not referencing `default.nix` (since it's changed to `package.nix`)
8. `outPath` doesn't change after migration

The tool is here: https://github.com/Aleksanaa/by-name-migrate.

pkgs/by-name/pr/pre-commit/pygrep-pythonpath.patch

@@ -0,0 +1,13 @@
+diff --git a/pre_commit/languages/pygrep.py b/pre_commit/languages/pygrep.py
+index ec55560..44e08a1 100644
+--- a/pre_commit/languages/pygrep.py
++++ b/pre_commit/languages/pygrep.py
+@@ -98,7 +98,7 @@ def run_hook(
+         color: bool,
+ ) -> tuple[int, bytes]:
+     cmd = (sys.executable, '-m', __name__, *args, entry)
+-    return xargs(cmd, file_args, color=color)
++    return xargs(cmd, file_args, color=color, env={ "PYTHONPATH": ':'.join(sys.path) })
+ 
+ 
+ def main(argv: Sequence[str] | None = None) -> int: