treewide(small-scale): remove with lib from meta, files with biggest diff

[lucasew]

Part of #371862

• eclipse: remove with lib in meta
• octoprint: remove with lib in meta
• cpython: remove with lib in meta, remove top level with
• hunspell/dictionaries: remove with lib in meta
• indilib: remove with lib in meta
• tmux-plugins: remove with lib in meta
• nginx/modules: remove with lib in meta
• perlPackages: remove with lib in meta

Things done

• Built on platform(s)
  • 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
• Tested basic functionality of all binary files (usually in ./result/bin/)
• 25.05 Release Notes (or backporting 24.11 and 25.05 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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[wolfgangwalther]

Superseded by #443046.