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

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

@@ -0,0 +1,57 @@
+{
+  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";
+            };
+          };
+        };
+      };
+    };
+  };
+}