Update packages in nix.

nix/configuration/configuration.nix

@@ -113,6 +113,11 @@
       # "git-hashing"
     ];
     nix.settings.trusted-users = [ "@wheel" ];
+    nix.settings.connect-timeout = 5;
+    nix.settings.min-free = 128000000;
+    nix.settings.max-free = 1000000000;
+    nix.settings.fallback = true;
+    nix.settings.warn-dirty = false;
 
     hardware.enableRedistributableFirmware = true;
 
@@ -161,6 +166,7 @@
     nixpkgs.overlays =
       let
         disableTests = (
+          # Example: (disableTests "coreutils")
           package_name:
           (final: prev: {
             "${package_name}" = prev."${package_name}".overrideAttrs (old: {
@@ -169,23 +175,65 @@
             });
           })
         );
+        disableTestsPython = (
+          # Example: (disableTestsPython "scipy")
+          package_name:
+          (final: prev: {
+            pythonPackagesExtensions = prev.pythonPackagesExtensions ++ [
+              (python-final: python-prev: {
+                "${package_name}" = python-prev."${package_name}".overridePythonAttrs (oldAttrs: {
+                  doCheck = false;
+                });
+              })
+            ];
+          })
+        );
+        disableOptimizations = (
+          # Example: (disableOptimizations "coreutils")
+          package_name:
+          (final: prev: {
+            "${package_name}" = final.unoptimized."${package_name}";
+          })
+        );
+        disableOptimizationsScope = (
+          # Example: (disableOptimizationsScope "kdePackages" "qtbase")
+          scope: package_name:
+          (final: prev: {
+            "${scope}" = prev."${scope}".overrideScope (
+              scopeFinal: scopePrev: {
+                "${package_name}" = final.unoptimized."${scope}"."${package_name}";
+              }
+            );
+          })
+        );
+        disableOptimizationsPython3 = (
+          # Example: (disableOptimizationsPython3 "scipy")
+          package_name:
+          (final: prev: {
+            python3Packages = prev.python3Packages.override {
+              overrides = python-final: python-prev: {
+                "${package_name}" = final.unoptimized.python3.pkgs."${package_name}";
+              };
+            };
+          })
+        );
       in
       [
+        (disableTests "coreutils")
+        (disableTests "coreutils-full")
+        (disableTests "libuv")
+        (final: prev: {
+          inherit (final.unoptimized) libtpms libjxl;
+        })
+        (disableOptimizationsPython3 "scipy")
+        # Works but probably sets python2's scipy to be python3:
+        #
         # (final: prev: {
-        #   imagemagick = prev.imagemagick.overrideAttrs (old: rec {
-        #     # 7.1.2-6 seems to no longer exist, so use 7.1.2-7
-        #     version = "7.1.2-7";
-
-        #     src = final.fetchFromGitHub {
-        #       owner = "ImageMagick";
-        #       repo = "ImageMagick";
-        #       tag = version;
-        #       hash = "sha256-9ARCYftoXiilpJoj+Y+aLCEqLmhHFYSrHfgA5DQHbGo=";
-        #     };
-        #   });
+        #   pythonPackagesExtensions = prev.pythonPackagesExtensions ++ [
+        #     (python-final: python-prev: {
+        #       scipy = final.unoptimized.python3Packages.scipy;
         #     })
-        # (final: prev: {
-        #   grub2 = (final.callPackage ./package/grub { });
+        #   ];
         # })
       ];
 

nix/configuration/flake.lock

@@ -22,11 +22,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1764110879,
-        "narHash": "sha256-xanUzIb0tf3kJ+PoOFmXEXV1jM3PjkDT/TQ5DYeNYRc=",
+        "lastModified": 1769524058,
+        "narHash": "sha256-zygdD6X1PcVNR2PsyK4ptzrVEiAdbMqLos7utrMDEWE=",
         "owner": "nix-community",
         "repo": "disko",
-        "rev": "aecba248f9a7d68c5d1ed15de2d1c8a4c994a3c5",
+        "rev": "71a3fc97d80881e91710fe721f1158d3b96ae14d",
         "type": "github"
       },
       "original": {
@@ -94,13 +94,40 @@
         "type": "github"
       }
     },
-    "impermanence": {
+    "home-manager": {
+      "inputs": {
+        "nixpkgs": [
+          "impermanence",
+          "nixpkgs"
+        ]
+      },
       "locked": {
-        "lastModified": 1737831083,
-        "narHash": "sha256-LJggUHbpyeDvNagTUrdhe/pRVp4pnS6wVKALS782gRI=",
+        "lastModified": 1768598210,
+        "narHash": "sha256-kkgA32s/f4jaa4UG+2f8C225Qvclxnqs76mf8zvTVPg=",
+        "owner": "nix-community",
+        "repo": "home-manager",
+        "rev": "c47b2cc64a629f8e075de52e4742de688f930dc6",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-community",
+        "repo": "home-manager",
+        "type": "github"
+      }
+    },
+    "impermanence": {
+      "inputs": {
+        "home-manager": "home-manager",
+        "nixpkgs": [
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1769548169,
+        "narHash": "sha256-03+JxvzmfwRu+5JafM0DLbxgHttOQZkUtDWBmeUkN8Y=",
         "owner": "nix-community",
         "repo": "impermanence",
-        "rev": "4b3e914cdf97a5b536a889e939fb2fd2b043a170",
+        "rev": "7b1d382faf603b6d264f58627330f9faa5cba149",
         "type": "github"
       },
       "original": {
@@ -137,11 +164,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1763966396,
-        "narHash": "sha256-6eeL1YPcY1MV3DDStIDIdy/zZCDKgHdkCmsrLJFiZf0=",
+        "lastModified": 1770197578,
+        "narHash": "sha256-AYqlWrX09+HvGs8zM6ebZ1pwUqjkfpnv8mewYwAo+iM=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "5ae3b07d8d6527c42f17c876e404993199144b6a",
+        "rev": "00c21e4c93d963c50d4c0c89bfa84ed6e0694df2",
         "type": "github"
       },
       "original": {

nix/configuration/flake.nix

@@ -15,7 +15,10 @@
   description = "My system configuration";
 
   inputs = {
-    impermanence.url = "github:nix-community/impermanence";
+    impermanence = {
+      url = "github:nix-community/impermanence";
+      inputs.nixpkgs.follows = "nixpkgs";
+    };
     nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
     lanzaboote = {
       url = "github:nix-community/lanzaboote/v0.4.2";

nix/configuration/formats/installer.nix

@@ -37,7 +37,8 @@ in
     (modulesPath + "/profiles/all-hardware.nix")
   ];
 
-  boot.kernelPackages = pkgs.linuxPackagesFor pkgs.linux_6_17;
+  boot.kernelPackages = pkgs.linuxPackagesFor pkgs.linux_6_18;
+  # boot.kernelPackages = pkgs.linuxPackagesFor pkgs.linux;
   boot.zfs.package = pkgs.zfs_unstable;
   boot.kernelParams = [
     "quiet"

nix/configuration/roles/base/default.nix

@@ -57,7 +57,7 @@ in
       ipcalc
       gptfdisk # for cgdisk
       nix-output-monitor # For better view into nixos-rebuild
-      nix-serve-ng # Serve nix store over http
+      # nix-serve-ng # Serve nix store over http
       cleanup_temporary_files
       jq
       inetutils # For whois

nix/configuration/roles/emacs/default.nix

@@ -125,7 +125,7 @@ in
                       ]
                     ))
                     final.nixd # nix language server
-                    final.nixfmt-rfc-style # auto-formatting nix files through nixd
+                    final.nixfmt # auto-formatting nix files through nixd
                     final.clang # To compile tree-sitter grammars
                     final.shellcheck
                     final.cmake-language-server

nix/configuration/roles/gpg/default.nix

@@ -44,11 +44,11 @@ in
     ];
     services.pcscd.enable = true;
 
-    me.install.user.talexander.file = {
-      ".gnupg/scdaemon.conf" = {
-        source = ./files/scdaemon.conf;
-      };
-    };
+    # me.install.user.talexander.file = {
+    #   ".gnupg/scdaemon.conf" = {
+    #     source = ./files/scdaemon.conf;
+    #   };
+    # };
 
     programs.gnupg.agent = {
       enable = true;

nix/configuration/roles/network/default.nix

@@ -37,9 +37,9 @@
     services.resolved = {
       enable = true;
       # dnssec = "true";
-      domains = [ "~." ];
-      fallbackDns = [ ];
-      dnsovertls = "true";
+      settings.Resolve.Domains = [ "~." ];
+      settings.Resolve.FallbackDNS = [ ];
+      settings.Resolve.DNSOverTLS = "true";
     };
 
     # Without this, systemd-resolved will send DNS requests for <X>.home.arpa to the per-link DNS server (172.16.0.1) which does not support DNS-over-TLS. This leads to the connection hanging and timing out. This causes firefox startup to take an extra 10+ seconds.

nix/configuration/roles/optimized_build/default.nix

@@ -52,7 +52,8 @@
     (lib.mkIf (!config.me.optimizations.enable) (
       lib.mkMerge [
         {
-          boot.kernelPackages = pkgs.linuxPackagesFor pkgs.linux_6_17;
+          boot.kernelPackages = pkgs.linuxPackagesFor pkgs.linux_6_18;
+          # boot.kernelPackages = pkgs.linuxPackagesFor pkgs.linux;
         }
       ]
     ))
@@ -90,7 +91,7 @@
                   HZ = lib.kernel.freeform "300";
                   HZ_300 = lib.kernel.yes;
                   HZ_1000 = lib.kernel.no;
-                } prev.linux_6_17;
+                } prev.linux_6_18; # or prev.linux
               }
             )
             (final: prev: {

nix/configuration/roles/rust/default.nix

@@ -50,9 +50,9 @@ in
       ".cargo/config.toml" = {
         source = ./files/cargo_config.toml;
       };
-      ".rustup/settings.toml" = {
-        source = ./files/rustup_settings.toml;
-      };
+      # ".rustup/settings.toml" = {
+      #   source = ./files/rustup_settings.toml;
+      # };
     };
 
     environment.persistence."/state" = lib.mkIf (config.me.mountPersistence) {

nix/configuration/roles/ssh/default.nix

@@ -30,7 +30,6 @@
         ];
       };
       users.root = {
-        home = "/root";
         files = [
           ".ssh/known_hosts"
         ];
@@ -47,5 +46,9 @@
         source = ./files/ssh_config;
       };
     };
+
+    programs.ssh.extraConfig = ''
+      Include ${./files/ssh_config_global}
+    '';
   };
 }

nix/configuration/roles/ssh/files/ssh_config

@@ -37,6 +37,3 @@ Host hydra
 Host i_only_boot_zfs
   HostName 127.0.0.1
   Port 60022
-
-Host *
-  Compression yes

nix/configuration/roles/ssh/files/ssh_config_global

@@ -0,0 +1,4 @@
+Host *
+  Compression yes
+  # ServerAliveInterval 240
+  # TCPKeepAlive yes # Default is yes

nix/configuration/roles/ssh/files/ssh_config_root

@@ -4,6 +4,3 @@ Host hydra
   User nixworker
   IdentitiesOnly yes
   IdentityFile /persist/manual/ssh/root/keys/id_ed25519
-
-Host *
-  Compression yes

nix/configuration/roles/sshd/default.nix

@@ -22,6 +22,9 @@
       settings = {
         PasswordAuthentication = false;
         KbdInteractiveAuthentication = false;
+        # ClientAliveInterval = 120;
+        # ClientAliveCountMax = 3;
+        # TCPKeepAlive = "yes"; # Default is yes
       };
       hostKeys = [
         {

nix/configuration/util/install_files/default.nix

@@ -11,7 +11,7 @@ let
     attrNames
     ;
 
-  get_shell_values =
+  get_user_shell_values =
     target:
     let
       homedir = config.users.users."${target.username}".home;
@@ -25,6 +25,19 @@ let
       username = lib.strings.escapeShellArg "${target.username}";
       group = lib.strings.escapeShellArg "${group}";
     };
+  get_global_shell_values =
+    target:
+    let
+      group = config.users.users."${target.username}".group;
+    in
+    {
+      source = lib.strings.escapeShellArg "${target.source}";
+      destination = lib.strings.escapeShellArg "${target.target}";
+      mode = lib.strings.escapeShellArg "${target.mode}";
+      dir_mode = lib.strings.escapeShellArg "${target.dir_mode}";
+      username = lib.strings.escapeShellArg "${target.username}";
+      group = lib.strings.escapeShellArg "${group}";
+    };
   install_user_file =
     let
       constructors = {
@@ -33,12 +46,20 @@ let
       };
     in
     stage: target: (constructors."${target.method}"."${stage}" target);
+  install_global_file =
+    let
+      constructors = {
+        "overwrite" = install_global_file_overwrite;
+        "symlink" = install_global_file_symlink;
+      };
+    in
+    stage: target: (constructors."${target.method}"."${stage}" target);
   install_user_file_overwrite = {
     "check" = (target: "");
     "install" = (
       target:
       let
-        inherit (get_shell_values target)
+        inherit (get_user_shell_values target)
           source
           destination
           mode
@@ -79,7 +100,7 @@ let
     "uninstall" = (
       target:
       let
-        inherit (get_shell_values target)
+        inherit (get_user_shell_values target)
           source
           destination
           ;
@@ -107,7 +128,7 @@ let
     "install" = (
       target:
       let
-        inherit (get_shell_values target)
+        inherit (get_user_shell_values target)
           source
           destination
           mode
@@ -151,7 +172,7 @@ let
     "uninstall" = (
       target:
       let
-        inherit (get_shell_values target)
+        inherit (get_user_shell_values target)
           source
           destination
           ;
@@ -174,21 +195,148 @@ let
         ]
     );
   };
-in
-{
-  imports = [ ];
-
-  options.me.install = {
-    user = lib.mkOption {
-      default = { };
-      type = lib.types.attrsOf (
-        lib.types.submodule (
-          { name, config, ... }:
+  install_global_file_overwrite = {
+    "check" = (target: "");
+    "install" = (
+      target:
       let
-            username = name;
+        inherit (get_global_shell_values target)
+          source
+          destination
+          mode
+          dir_mode
+          username
+          group
+          ;
+        flags = lib.strings.concatStringsSep " " [
+          (if mode != "" then "-m ${mode}" else "")
+          (if username != "" then "-o ${username}" else "")
+          (if group != "" then "-g ${group}" else "")
+        ];
+        dir_flags = lib.strings.concatStringsSep " " [
+          (if dir_mode != "" then "-m ${dir_mode}" else "")
+          (if username != "" then "-o ${username}" else "")
+          (if group != "" then "-g ${group}" else "")
+        ];
       in
-          {
-            options = {
+      if target.recursive then
+        [
+          ''
+            find ${source} -type f -print0 | while read -r -d "" file; do
+                relative_path=$(realpath -s --relative-to ${source} "$file")
+                full_dest=${destination}/"$relative_path"
+                create_containing_directories "$full_dest" ${dir_flags}
+                $DRY_RUN_CMD install $VERBOSE_ARG --compare ${flags} "$file" "$full_dest"
+            done
+          ''
+        ]
+      else
+        [
+          ''
+            create_containing_directories ${destination} ${dir_flags}
+            $DRY_RUN_CMD install $VERBOSE_ARG --compare ${flags} ${source} ${destination}
+          ''
+        ]
+    );
+    "uninstall" = (
+      target:
+      let
+        inherit (get_global_shell_values target)
+          source
+          destination
+          ;
+      in
+      if target.recursive then
+        [
+          ''
+            find ${source} -type f -print0 | while read -r -d "" file; do
+                relative_path=$(realpath -s --relative-to ${source} "$file")
+                full_dest=${destination}/"$relative_path"
+                $DRY_RUN_CMD echo rm -f "$full_dest"
+            done
+          ''
+        ]
+      else
+        [
+          ''
+            $DRY_RUN_CMD echo rm -f ${destination}
+          ''
+        ]
+    );
+  };
+  install_global_file_symlink = {
+    "check" = (target: "");
+    "install" = (
+      target:
+      let
+        inherit (get_global_shell_values target)
+          source
+          destination
+          mode
+          dir_mode
+          username
+          group
+          ;
+        owner = lib.strings.concatStringsSep ":" (
+          filter (val: val != "") [
+            username
+            group
+          ]
+        );
+        dir_flags = lib.strings.concatStringsSep " " [
+          (if dir_mode != "" then "-m ${dir_mode}" else "")
+          (if username != "" then "-o ${username}" else "")
+          (if group != "" then "-g ${group}" else "")
+        ];
+      in
+      if target.recursive then
+        [
+          ''
+            find ${source} -type f -print0 | while read -r -d "" file; do
+                relative_path=$(realpath -s --relative-to ${source} "$file")
+                full_dest=${destination}/"$relative_path"
+                create_containing_directories "$full_dest" ${dir_flags}
+                $DRY_RUN_CMD ln $VERBOSE_ARG -s "$file" "$full_dest"
+                $DRY_RUN_CMD chown $VERBOSE_ARG -h ${owner} "$full_dest"
+            done
+          ''
+        ]
+      else
+        [
+          ''
+            create_containing_directories ${destination} ${dir_flags}
+            $DRY_RUN_CMD ln $VERBOSE_ARG -s ${source} ${destination}
+            $DRY_RUN_CMD chown $VERBOSE_ARG -h ${owner} ${destination}
+          ''
+        ]
+    );
+    "uninstall" = (
+      target:
+      let
+        inherit (get_global_shell_values target)
+          source
+          destination
+          ;
+      in
+      if target.recursive then
+        [
+          ''
+            find ${source} -type f -print0 | while read -r -d "" file; do
+                relative_path=$(realpath -s --relative-to ${source} "$file")
+                full_dest=${destination}/"$relative_path"
+                $DRY_RUN_CMD echo rm -f "$full_dest"
+            done
+          ''
+        ]
+      else
+        [
+          ''
+            $DRY_RUN_CMD echo rm -f ${destination}
+          ''
+        ]
+    );
+  };
+  install_target_options = username: {
     enable = lib.mkOption {
       type = lib.types.bool;
       default = true;
@@ -198,6 +346,7 @@ in
     };
 
     file = lib.mkOption {
+      default = { };
       type = lib.types.attrsOf (
         lib.types.submodule (
           { name, config, ... }:
@@ -274,11 +423,29 @@ in
       );
     };
   };
+in
+{
+  imports = [ ];
+
+  options.me.install = (
+    {
+      user = lib.mkOption {
+        default = { };
+        type = lib.types.attrsOf (
+          lib.types.submodule (
+            { name, config, ... }:
+            let
+              username = name;
+            in
+            {
+              options = (install_target_options username);
             }
           )
         );
       };
-  };
+    }
+    // (install_target_options "root")
+  );
 
   config =
     let
@@ -288,11 +455,17 @@ in
         builtins.map (user: (builtins.map (path: user.file."${path}") (attrNames user.file))) enabled_users
       );
       enabled_file_targets = filter (target: target.enable) all_file_targets;
-      check_commands = lib.flatten (builtins.map (install_user_file "check") enabled_file_targets);
-      install_commands = lib.flatten (builtins.map (install_user_file "install") enabled_file_targets);
-      uninstall_commands = lib.flatten (
-        builtins.map (install_user_file "uninstall") enabled_file_targets
-      );
+      all_global_file_targets = (builtins.map (path: cfg.file."${path}") (attrNames cfg.file));
+      enabled_global_file_targets = filter (target: target.enable) all_global_file_targets;
+      check_commands =
+        (lib.flatten (builtins.map (install_global_file "check") enabled_global_file_targets))
+        ++ (lib.flatten (builtins.map (install_user_file "check") enabled_file_targets));
+      install_commands =
+        (lib.flatten (builtins.map (install_global_file "install") enabled_global_file_targets))
+        ++ (lib.flatten (builtins.map (install_user_file "install") enabled_file_targets));
+      uninstall_commands =
+        (lib.flatten (builtins.map (install_global_file "uninstall") enabled_global_file_targets))
+        ++ (lib.flatten (builtins.map (install_user_file "uninstall") enabled_file_targets));
     in
     {
       systemd.services.me-install-file = {