spades: 3.15.5 -> 4.0.0

[bzizou]

Description of changes

Upgrade to Spades 4.0.0

• compilation bug with gcc 13 has been fixed upstream
• copytree.patch will be suggested upstream, but not sure if they will care as it is relatively related to Nix: the spades pipeline copies some config data that are in the tree of spades, and of course into nix, the u+w mode is removed, and the copy preserves the modes, so there's a "permission denied" error (easy to see with spades.py --test)

Things done

• Built on platform(s)
  • [X] x86_64-linux
  • [ ] aarch64-linux
  • [ ] x86_64-darwin
  • [ ] aarch64-darwin
• For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)
  • [ ] sandbox = relaxed
  • [ ] sandbox = true
• [ ] Tested, as applicable:
  • NixOS test(s) (look inside nixos/tests)
  • and/or package tests
  • or, for functions and "core" functionality, tests in lib/tests or pkgs/test
  • made sure NixOS tests are linked to the relevant packages
• [ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
• [X] Tested basic functionality of all binary files (usually in ./result/bin/) ---> ./result/bin/spades.py --test
• 24.11 Release Notes (or backporting 23.11 and 24.05 Release notes)
  • [ ] (Package updates) Added a release notes entry if the change is major or breaking
  • [ ] (Module updates) Added a release notes entry if the change is significant
  • [ ] (Module addition) Added a release notes entry if adding a new NixOS module
• [ ] Fits CONTRIBUTING.md.

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