treewide: Change URLs to HTTPS

Lots of URLs were HTTP redirect to HTTPS. Changed those and checked them
if there's actual content. Inspired by
https://github.com/NixOS/nixpkgs/issues/60004

pkgs/development/python-modules/nibabel/default.nix

@@ -38,7 +38,7 @@ buildPythonPackage rec {
   '';
 
   meta = with lib; {
-    homepage = http://nipy.org/nibabel/;
+    homepage = https://nipy.org/nibabel/;
     description = "Access a multitude of neuroimaging data formats";
     license = licenses.mit;
     maintainers = with maintainers; [ ashgillman ];