refactor(modules): flatten directory structure to 2-level category layout

[RAPSNX]

Summary

• Flatten module directory layout to a 2-level category hierarchy (modules/<target>/<category>/<module>.nix), removing single-file nested directories and lonely default.nix wrappers.
• Update flake.nix to load modules automatically using inputs.import-tree ./modules/nixos and inputs.import-tree ./modules/home.
• Remove redundant boilerplate aggregator default.nix files.
• Retain asset directories (waybar/, swaync/, wlogout/) that bundle CSS, JSON, and icons.
• Update AGENTS.md and structure documentation to reflect the flattened layout.

Validation

• Evaluated all NixOS host configurations (zion, kubex, nixberry, vinox)
• Evaluated all Home Manager configurations (rap@zion, nix@firefly)
• Passed statix check ., deadnix ., and nixfmt