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/system/machines/desktop/modules/disko/default.nix

@@ -1,57 +0,0 @@
-{
-  disko.devices = {
-    disk = {
-      main = {
-        type = "disk";
-        device = "/dev/disk/by-id/ata-CT2000MX500SSD1_2137E5D2D47D";
-        content = {
-          type = "gpt";
-          partitions = {
-            boot = {
-              size = "1G";
-              type = "EF00";
-              content = {
-                type = "filesystem";
-                format = "vfat";
-                mountpoint = "/boot";
-                mountOptions = [ "umask=0077" ];
-              };
-            };
-            primary = {
-              size = "100%";
-              content = {
-                type = "lvm_pv";
-                vg = "nix";
-              };
-            };
-          };
-        };
-      };
-    };
-
-    lvm_vg = {
-      nix = {
-        type = "lvm_vg";
-        lvs = {
-          root = {
-            size = "5%";
-            content = {
-              type = "filesystem";
-              format = "ext4";
-              mountpoint = "/";
-              mountOptions = [ "defaults" ];
-            };
-          };
-          home = {
-            size = "100%FREE";
-            content = {
-              type = "filesystem";
-              format = "ext4";
-              mountpoint = "/home";
-            };
-          };
-        };
-      };
-    };
-  };
-}