refactor: reorganize flake structure and consolidate user config

Directory structure:
- Move from src/ to root level (system/, user/)
- Remove unused machines (workstation, vm, laptop)

User configuration:
- Add user/home.nix for shared defaults (pass, essentials, default modules)
- Centralize user options in user/default.nix
- Move submodules to consistent paths (bash/bash, git/git, neovim/nvim, vim/vim)

Module reorganization:
- Flatten nested module structures (remove /modules/ subdirs)
- Split CLI vs GUI tools (dev/ for CLI, gui/dev/ for GUI)
- Move neovim/vim to top-level modules (not under utils/)
- Remove security.enable - pass now in user/home.nix
- Remove utils.enable - essentials now in user/home.nix
- Add security/yubikey module with yubikey-manager, age-plugin-yubikey
- Move pcb, design to gui/dev/
- Replace penpot docker wrapper with nixpkgs penpot-desktop
- Remove i3 config
- Remove deprecated wsl.nativeSystemd option

GUI improvements:
- Browser-focused mimeApps in gui/default.nix
- Each WM handles its own auto-start via profileExtra

Cleanup:
- Update README with new structure
- Update justfile paths and valid systems
- Fix submodule paths in .gitmodules

src/user/config/keys/default.nix

@@ -1,33 +0,0 @@
-{ lib }:
-
-with builtins;
-let
-  extractName = filename:
-    let
-      # Remove .key extension
-      noKey = lib.removeSuffix ".key" filename;
-      # Remove .pub/.priv/.public/.private markers
-      noMarkers = replaceStrings
-        [ ".pub" ".priv" ".public" ".private" ]
-        [ "" "" "" "" ]
-        noKey;
-    in noMarkers;
-
-  constructKeys = dir: (
-    listToAttrs (
-      map (subdir: {
-        name = subdir;
-        value = listToAttrs (
-          map (file: {
-            name = extractName file;
-            value = readFile "${dir}/${subdir}/${file}";
-          }) (filter (file:
-            (readDir "${dir}/${subdir}").${file} == "regular" &&
-            lib.hasSuffix ".key" file
-          ) (attrNames (readDir "${dir}/${subdir}")))
-        );
-      }) (filter (node: (readDir dir).${node} == "directory") (attrNames (readDir dir)))
-    )
-  );
-in
-  constructKeys ./.