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/nipype/default.nix

@@ -97,7 +97,7 @@ buildPythonPackage rec {
   doCheck = false;
 
   meta = with stdenv.lib; {
-    homepage = http://nipy.org/nipype/;
+    homepage = https://nipy.org/nipype/;
     description = "Neuroimaging in Python: Pipelines and Interfaces";
     license = licenses.bsd3;
     maintainers = with maintainers; [ ashgillman ];