fix(nix): resolve stdenv deprecation warnings and gemini-cli deprecation

docs/CHANGELOG.md

@@ -1,7 +1,20 @@
 # Changelog
 
+## 2026-08-25
+
+- Fixed Nix evaluation warnings for `stdenv` deprecation and `gemini-cli`:
+  - Replaced deprecated `stdenv.isLinux` and `stdenv.isDarwin` checks across module presets and package definitions with `stdenv.hostPlatform.isLinux` and `stdenv.hostPlatform.isDarwin`.
+  - Replaced deprecated `pkgs.gemini-cli` with `pkgs.antigravity-cli` (and updated binary invocation to `agy`) in `experimental.nix` profile and `daily-summary.nix` launchd service.
+
+## 2026-08-25
+
+- Fixed multi-second hang and permanent typing latency in Fish after exiting TUIs inside Zellij and Ghostty:
+  - Exported `fish_features = "no-query-term"` in `home.sessionVariables` and added `set -gx fish_features no-query-term` to Fish's top-level `shellInit`. Previous attempt (`set -a fish_features no-query-term` in `interactiveShellInit`) set a local variable inside an anonymous initialization function block that went out of scope immediately after startup. Furthermore, Fish reads `fish_features` at binary launch before interactive init functions run. Without `no-query-term` exported prior to Fish startup, Fish attempted terminal feature queries (Primary Device Attributes `DA1` / `\e[?c` and termcap) whenever a TUI (e.g. Neovim, Lazygit, Yazi) exited and returned control to Fish. Zellij drops or delays DA1 response sequences, causing Fish to block on a multi-second stdin timeout, followed by severe input reader desynchronization and typing latency on every subsequent keystroke.
+  - Disabled `programs.ghostty.enableFishIntegration` and conditionally sourced Ghostty's shell integration script in `shellInit` only when NOT running inside a multiplexer (`not set -q ZELLIJ` and `not set -q TMUX`). Sourcing Ghostty's shell integration inside Zellij sent duplicate and conflicting OSC 133 prompt markers and DECSCUSR cursor escape sequences to Zellij's PTY parser.
+
 ## 2026-08-16
 
+- Fixed Zellij new tab directory tracking by adding `__fish_update_cwd_osc` override in `presets/programs/zellij.nix`. Fish's default OSC 7 sequence includes `$hostname`, which on macOS or dynamic network environments evaluates to `Noah-MacBook-Pro.local` or a domain suffix. Zellij compares the OSC 7 hostname against its system hostname (`Noah-MacBook-Pro`), finds a mismatch, and silently ignores the CWD update, leaving new tabs stuck in a previous directory or session default. Overriding `__fish_update_cwd_osc` to send `file://<PWD>` (empty hostname) ensures Zellij always updates its cached CWD on every `cd` and prompt render.
 - Fixed Firefox "profile cannot be loaded" error on macOS by removing `home.file."Library/Application Support/Firefox/installs.ini"`. Hardcoding an installation hash in `installs.ini` broke whenever Firefox was updated or rebuilt in the Nix store because the nix store path changed, causing Firefox to compute a new installation hash, fail to match or write to the read-only `installs.ini` symlink, and error out. Firefox on macOS uses `profiles.ini` (managed by Home Manager) and `MOZ_LEGACY_PROFILES=1` (exported by nixpkgs' launcher wrapper).
 
 ## 2026-08-03

pkgs/applications/misc/volnoti/package.nix

@@ -1,7 +1,7 @@
 # Fix: Volnoti error: 'volnoti' has been removed due to lack of maintenance upstream.
 
 { pkgs, lib, ... }:
-if !pkgs.stdenv.isLinux then
+if !pkgs.stdenv.hostPlatform.isLinux then
   null
 else
 pkgs.stdenv.mkDerivation {

pkgs/slsk-batchdl/package.nix

@@ -6,7 +6,7 @@
   dotnetCorePackages,
 }:
 
-if !stdenv.isLinux then
+if !stdenv.hostPlatform.isLinux then
   null
 else
   buildDotnetModule rec {

pkgs/tools/misc/installer/package.nix

@@ -3,7 +3,7 @@
 # Inspired by https://github.com/cleverca22/nix-tests/blob/master/kexec/justdoit.nix
 # This script will partition and format drives; use at your own risk!
 
-if !pkgs.stdenv.isLinux then
+if !pkgs.stdenv.hostPlatform.isLinux then
   null
 else
   pkgs.writeShellScriptBin "installer" ''

pkgs/tools/misc/rebuild/package.nix

@@ -2,7 +2,7 @@
 
 pkgs.writeShellScriptBin "rebuild" ''
   echo ${pkgs.stdenv.hostPlatform.system}
-  SYSTEM=${if pkgs.stdenv.isDarwin then "darwin" else "linux"}
+  SYSTEM=${if pkgs.stdenv.hostPlatform.isDarwin then "darwin" else "linux"}
   if [ "$SYSTEM" == "darwin" ]; then
       sudo darwin-rebuild switch --flake ${builtins.toString ../../../../.}
   else

platforms/home-manager/modules/nmasur/presets/programs/_1password.nix

@@ -23,7 +23,7 @@ in
     home.packages = [
       pkgs._1password-cli
     ]
-    ++ (if pkgs.stdenv.isLinux then [ pkgs._1password-gui ] else [ ]);
+    ++ (if pkgs.stdenv.hostPlatform.isLinux then [ pkgs._1password-gui ] else [ ]);
 
     # # Firefox extension
     # programs.firefox.profiles.default.extensions.packages = [

platforms/home-manager/modules/nmasur/presets/programs/aerc.nix

@@ -203,13 +203,13 @@ in
     };
 
     # Used for macOS
-    xdg.enable = lib.mkIf pkgs.stdenv.isDarwin true;
+    xdg.enable = lib.mkIf pkgs.stdenv.hostPlatform.isDarwin true;
 
-    xdg.desktopEntries.aerc = lib.mkIf (pkgs.stdenv.isLinux) {
+    xdg.desktopEntries.aerc = lib.mkIf (pkgs.stdenv.hostPlatform.isLinux) {
       name = "aerc";
       exec = "${lib.getExe config.nmasur.presets.services.i3.terminal} -e aerc %u";
     };
-    xsession.windowManager.i3.config.keybindings = lib.mkIf pkgs.stdenv.isLinux {
+    xsession.windowManager.i3.config.keybindings = lib.mkIf pkgs.stdenv.hostPlatform.isLinux {
       "${config.xsession.windowManager.i3.config.modifier}+Shift+e" =
         let
           terminal = config.nmasur.presets.services.i3.terminal;

platforms/home-manager/modules/nmasur/presets/programs/calibre.nix

@@ -14,12 +14,12 @@ in
   options.nmasur.presets.programs.calibre.enable = lib.mkEnableOption "Calibre e-book manager";
 
   config = lib.mkIf cfg.enable {
-    home.packages = lib.mkIf pkgs.stdenv.isLinux [ pkgs.calibre ];
+    home.packages = lib.mkIf pkgs.stdenv.hostPlatform.isLinux [ pkgs.calibre ];
     home.sessionVariables = {
       CALIBRE_USE_DARK_PALETTE = 1;
     };
 
-    home.file.".Brewfile".text = lib.mkIf pkgs.stdenv.isDarwin /* homebrew */ ''
+    home.file.".Brewfile".text = lib.mkIf pkgs.stdenv.hostPlatform.isDarwin /* homebrew */ ''
       cask "calibre" # Nix package broken on macOS
     '';
 

platforms/home-manager/modules/nmasur/presets/programs/chawan.nix

@@ -18,7 +18,7 @@ in
     programs.chawan = {
       enable = true;
       settings = {
-        external.copy-cmd = if pkgs.stdenv.isLinux then "xclip -selection clipboard -in" else "pbcopy";
+        external.copy-cmd = if pkgs.stdenv.hostPlatform.isLinux then "xclip -selection clipboard -in" else "pbcopy";
       };
     };
 

platforms/home-manager/modules/nmasur/presets/programs/firefox.nix

@@ -25,7 +25,7 @@ in
       enable = true;
       package = pkgs.firefox;
       # Use appropriate default path depending on the OS
-      configPath = if pkgs.stdenv.isDarwin then "Library/Application Support/Firefox" else ".mozilla/firefox";
+      configPath = if pkgs.stdenv.hostPlatform.isDarwin then "Library/Application Support/Firefox" else ".mozilla/firefox";
       profiles.default = {
         id = 0;
         name = "default";
@@ -57,7 +57,7 @@ in
           "app.update.auto" = false;
           "browser.aboutConfig.showWarning" = false;
           "browser.warnOnQuit" = false;
-          "browser.quitShortcut.disabled" = if pkgs.stdenv.isLinux then true else false;
+          "browser.quitShortcut.disabled" = if pkgs.stdenv.hostPlatform.isLinux then true else false;
           "browser.theme.dark-private-windows" = true;
           "browser.toolbars.bookmarks.visibility" = false;
           "browser.startup.page" = 3; # Restore previous session
@@ -189,7 +189,7 @@ in
 
     };
 
-    xsession.windowManager.i3.config.keybindings = lib.mkIf pkgs.stdenv.isLinux {
+    xsession.windowManager.i3.config.keybindings = lib.mkIf pkgs.stdenv.hostPlatform.isLinux {
       "${config.xsession.windowManager.i3.config.modifier}+Shift+b" = "exec ${
         # Don't name the script `firefox` or it will affect grep
         toString (

platforms/home-manager/modules/nmasur/presets/programs/fish.nix

@@ -69,9 +69,6 @@ in
         set -g fish_cursor_insert line
         set -g fish_cursor_visual block
         set -g fish_cursor_replace_one underscore
-
-        # Fix for lagging after exiting TUIs with Zellij and Ghostty
-        set -a fish_features no-query-term
       '';
       loginShellInit = "";
       shellAbbrs = {
@@ -117,10 +114,17 @@ in
         dr = "docker run --rm -it";
         db = "docker build . -t";
       };
-      shellInit = "";
+      shellInit = ''
+        # Fix for lagging/hanging after exiting TUIs inside terminal multiplexers like Zellij:
+        # Disable fish terminal querying at startup so fish does not query DA1/termcap on return.
+        set -gx fish_features no-query-term
+      '';
     };
 
-    home.sessionVariables.fish_greeting = "";
+    home.sessionVariables = {
+      fish_greeting = "";
+      fish_features = "no-query-term";
+    };
 
   };
 }

platforms/home-manager/modules/nmasur/presets/programs/ghostty.nix

@@ -21,9 +21,9 @@ in
     programs.ghostty = {
       enable = true;
 
-      package = if pkgs.stdenv.isDarwin then pkgs.ghostty-bin else pkgs.ghostty;
+      package = if pkgs.stdenv.hostPlatform.isDarwin then pkgs.ghostty-bin else pkgs.ghostty;
 
-      enableFishIntegration = true;
+      enableFishIntegration = false; # Handled conditionally below to avoid conflicts inside Zellij/TMUX
       enableBashIntegration = true;
       enableZshIntegration = true;
       installBatSyntax = false; # The file doesn't seem to exist in the pkg
@@ -33,8 +33,8 @@ in
         macos-titlebar-style = "hidden";
         window-decoration = false;
         macos-non-native-fullscreen = true;
-        quit-after-last-window-closed = lib.mkIf pkgs.stdenv.isDarwin true;
+        quit-after-last-window-closed = lib.mkIf pkgs.stdenv.hostPlatform.isDarwin true;
-        fullscreen = if pkgs.stdenv.isDarwin then true else false;
+        fullscreen = if pkgs.stdenv.hostPlatform.isDarwin then true else false;
         keybind = [
           "super+t=unbind" # Pass super-t to underlying tool (e.g. zellij tabs)
           "super+shift+]=unbind"
@@ -81,5 +81,12 @@ in
 
     };
 
+    # Conditionally enable Ghostty fish shell integration only when NOT running inside multiplexers like Zellij/TMUX
+    programs.fish.shellInit = ''
+      if set -q GHOSTTY_RESOURCES_DIR; and not set -q ZELLIJ; and not set -q TMUX
+        source "$GHOSTTY_RESOURCES_DIR/shell-integration/fish/vendor_conf.d/ghostty-shell-integration.fish"
+      end
+    '';
+
   };
 }

platforms/home-manager/modules/nmasur/presets/programs/helix.nix

@@ -723,7 +723,7 @@ in
     # Create a desktop option for launching Helix from a file manager
     # (Requires launching the terminal and then executing Helix)
     xdg.desktopEntries.helix =
-      lib.mkIf (pkgs.stdenv.isLinux && config.nmasur.presets.services.i3.enable)
+      lib.mkIf (pkgs.stdenv.hostPlatform.isLinux && config.nmasur.presets.services.i3.enable)
         {
           name = "Helix wrapper";
           exec = ''sh -c "${lib.getExe config.nmasur.presets.services.i3.terminal} --command='hx \$1'" _ %F ''; # TODO: change to work for any terminal

platforms/home-manager/modules/nmasur/presets/programs/kitty.nix

@@ -18,7 +18,7 @@ in
     nmasur.presets.services.i3.terminal = pkgs.kitty;
 
     # Set the Rofi terminal for running programs
-    programs.rofi.terminal = lib.mkIf pkgs.stdenv.isLinux (lib.mkDefault "${pkgs.kitty}/bin/kitty");
+    programs.rofi.terminal = lib.mkIf pkgs.stdenv.hostPlatform.isLinux (lib.mkDefault "${pkgs.kitty}/bin/kitty");
 
     # Display images in the terminal
     programs.fish.interactiveShellInit = # fish

platforms/home-manager/modules/nmasur/presets/programs/neovim.nix

@@ -63,7 +63,7 @@ in
     # Create a desktop option for launching Neovim from a file manager
     # (Requires launching the terminal and then executing Neovim)
     xdg.desktopEntries.nvim =
-      lib.mkIf (pkgs.stdenv.isLinux && config.nmasur.presets.services.i3.enable)
+      lib.mkIf (pkgs.stdenv.hostPlatform.isLinux && config.nmasur.presets.services.i3.enable)
         {
           name = "Neovim wrapper";
           exec = ''${lib.getExe config.nmasur.presets.services.i3.terminal} --command="nvim %F"''; # TODO: change to generic

platforms/home-manager/modules/nmasur/presets/programs/nixpkgs-darwin.nix

@@ -15,7 +15,7 @@ in
     description = "Nixpkgs tools for macOS";
     default =
       config.nmasur.presets.programs.nixpkgs.enable
-      && pkgs.stdenv.isDarwin
+      && pkgs.stdenv.hostPlatform.isDarwin
       && config.nmasur.presets.programs.dotfiles.enable;
   };
 

platforms/home-manager/modules/nmasur/presets/programs/noti.nix

@@ -13,7 +13,7 @@ in
 
   options.nmasur.presets.programs.noti.enable = lib.mkEnableOption "Noti CLI notifications";
 
-  config = lib.mkIf (cfg.enable && (pkgs.stdenv.isDarwin || config.services.dunst.enable)) {
+  config = lib.mkIf (cfg.enable && (pkgs.stdenv.hostPlatform.isDarwin || config.services.dunst.enable)) {
     home.packages = [ pkgs.noti ];
     programs.fish = {
       shellAbbrs = {

platforms/home-manager/modules/nmasur/presets/programs/starship.nix

@@ -42,7 +42,7 @@ in
         };
         cmd_duration = {
           min_time = 5001;
-          show_notifications = if pkgs.stdenv.isLinux then false else true;
+          show_notifications = if pkgs.stdenv.hostPlatform.isLinux then false else true;
           min_time_to_notify = 30000;
           format = "[$duration]($style) ";
         };

platforms/home-manager/modules/nmasur/presets/programs/wezterm.nix

@@ -105,7 +105,7 @@ in
         }
 
         config.font = wezterm.font('${cfg.font}', { weight = 'Bold'})
-        config.font_size = ${if pkgs.stdenv.isLinux then "14.0" else "18.0"}
+        config.font_size = ${if pkgs.stdenv.hostPlatform.isLinux then "14.0" else "18.0"}
 
         -- Fix color blocks instead of text
         config.front_end = "WebGpu"
@@ -114,7 +114,7 @@ in
         config.hide_tab_bar_if_only_one_tab = true
         config.window_frame = {
           font = wezterm.font('${cfg.font}', { weight = 'Bold'}),
-          font_size = ${if pkgs.stdenv.isLinux then "12.0" else "16.0"},
+          font_size = ${if pkgs.stdenv.hostPlatform.isLinux then "12.0" else "16.0"},
         }
 
         config.colors = {
@@ -191,7 +191,7 @@ in
           -- super-t open new tab in new dir
           {
             key = 't',
-            mods = ${if pkgs.stdenv.isDarwin then "'SUPER'" else "'ALT'"},
+            mods = ${if pkgs.stdenv.hostPlatform.isDarwin then "'SUPER'" else "'ALT'"},
             action = wezterm.action.SpawnCommandInNewTab {
               cwd = wezterm.home_dir,
             },

platforms/home-manager/modules/nmasur/presets/programs/zellij.nix

@@ -75,6 +75,17 @@ in
               ${lib.getExe pkgs.zellij} action new-pane --start-suspended -- gh run watch
             '';
         };
+        __fish_update_cwd_osc = {
+          description = "Notify Zellij/terminal of CWD changes without hostname mismatch";
+          body = # fish
+            ''
+              if test "$TERM" != "dumb"
+                  printf \e\]7\;file://%s\a (string escape --style=url -- $PWD)
+              end
+            '';
+          onVariable = "PWD";
+          onEvent = "fish_prompt";
+        };
       };
     };
 
@@ -129,17 +140,17 @@ in
         show_startup_tips = false;
 
         keybinds = {
-          locked = lib.mkIf (pkgs.stdenv.isLinux && !config.programs.ghostty.enable) {
+          locked = lib.mkIf (pkgs.stdenv.hostPlatform.isLinux && !config.programs.ghostty.enable) {
             # For servers that I SSH into, use c-a-G to unlock
-            "bind \"Ctrl Alt G\"" = lib.mkIf (pkgs.stdenv.isLinux && !config.programs.ghostty.enable) {
+            "bind \"Ctrl Alt G\"" = lib.mkIf (pkgs.stdenv.hostPlatform.isLinux && !config.programs.ghostty.enable) {
               SwitchToMode = {
                 _args = [ "normal" ];
               };
             };
           };
-          normal = lib.mkIf (pkgs.stdenv.isLinux && !config.programs.ghostty.enable) {
+          normal = lib.mkIf (pkgs.stdenv.hostPlatform.isLinux && !config.programs.ghostty.enable) {
             # For servers that I SSH into, use c-a-G to lock
-            "bind \"Ctrl Alt G\"" = lib.mkIf (pkgs.stdenv.isLinux && !config.programs.ghostty.enable) {
+            "bind \"Ctrl Alt G\"" = lib.mkIf (pkgs.stdenv.hostPlatform.isLinux && !config.programs.ghostty.enable) {
               SwitchToMode = {
                 _args = [ "locked" ];
               };
@@ -169,7 +180,7 @@ in
             "bind \"Alt Shift s\"" = {
               Run = {
                 _args =
-                  if pkgs.stdenv.isDarwin then
+                  if pkgs.stdenv.hostPlatform.isDarwin then
                     [
                       # "env"
                       # "PATH=/nix/var/nix/profiles/default/bin:/run/current-system/sw/bin:/usr/bin:/bin"
@@ -243,7 +254,7 @@ in
             "bind \"Alt Shift j\"" = {
               Run = {
                 _args =
-                  if pkgs.stdenv.isDarwin then
+                  if pkgs.stdenv.hostPlatform.isDarwin then
                     [
                       "env"
                       "PATH=${config.home.homeDirectory}/.nix-profile/bin:/etc/profiles/per-user/${username}/bin:/usr/bin"
@@ -284,24 +295,24 @@ in
             "bind \"Ctrl Shift Tab\"" = {
               GoToPreviousTab = { };
             };
-            "bind \"Super t\"" = lib.mkIf pkgs.stdenv.isDarwin {
+            "bind \"Super t\"" = lib.mkIf pkgs.stdenv.hostPlatform.isDarwin {
               NewTab = { };
             };
-            "bind \"Alt t\"" = lib.mkIf pkgs.stdenv.isLinux {
+            "bind \"Alt t\"" = lib.mkIf pkgs.stdenv.hostPlatform.isLinux {
               NewTab = { };
             };
-            "bind \"Super k\"" = lib.mkIf pkgs.stdenv.isDarwin {
+            "bind \"Super k\"" = lib.mkIf pkgs.stdenv.hostPlatform.isDarwin {
               SwitchToMode = {
                 _args = [ "scroll" ];
               };
             };
-            "bind \"Super Shift e\"" = lib.mkIf pkgs.stdenv.isDarwin {
+            "bind \"Super Shift e\"" = lib.mkIf pkgs.stdenv.hostPlatform.isDarwin {
               EditScrollback = { };
               SwitchToMode = {
                 _args = [ "locked" ];
               };
             };
-            "bind \"Alt Shift e\"" = lib.mkIf pkgs.stdenv.isLinux {
+            "bind \"Alt Shift e\"" = lib.mkIf pkgs.stdenv.hostPlatform.isLinux {
               EditScrollback = { };
               SwitchToMode = {
                 _args = [ "locked" ];

platforms/home-manager/modules/nmasur/presets/services/mbsync/mbsync.nix

@@ -43,14 +43,14 @@ in
     };
 
     # Automatically check for mail and keep files synced locally
-    services.mbsync = lib.mkIf pkgs.stdenv.isLinux {
+    services.mbsync = lib.mkIf pkgs.stdenv.hostPlatform.isLinux {
       enable = true;
       frequency = "*:0/5";
       postExec = "${lib.getExe pkgs.notmuch} new";
     };
 
     # Used to watch for new mail and trigger sync
-    services.imapnotify.enable = pkgs.stdenv.isLinux;
+    services.imapnotify.enable = pkgs.stdenv.hostPlatform.isLinux;
 
     # Allows sending email from CLI/sendmail
     programs.msmtp.enable = true;

platforms/home-manager/modules/nmasur/profiles/common.nix

@@ -15,7 +15,7 @@ in
 
     home.username = config.nmasur.settings.username;
     home.homeDirectory =
-      if pkgs.stdenv.isDarwin then "/Users/${config.home.username}" else "/home/${config.home.username}";
+      if pkgs.stdenv.hostPlatform.isDarwin then "/Users/${config.home.username}" else "/home/${config.home.username}";
 
     home.packages = [
       pkgs.dig # DNS lookup

platforms/home-manager/modules/nmasur/profiles/experimental.nix

@@ -40,7 +40,6 @@ in
 
       # LLM
 
-      pkgs.gemini-cli # AI LLM Agent
       pkgs.antigravity-cli # AI LLM Agent
       pkgs.pi-coding-agent # AI LLM Agent
 

platforms/nix-darwin/modules/nmasur/presets/services/daily-summary/daily-summary.nix

@@ -29,10 +29,10 @@ in
       # This replaces program and args entirely
       # script = ''
       #   ${process_urls}/bin/process-urls /Users/${username}/Downloads/Sidebery/
-      #   GEMINI_API_KEY=$(cat /Users/${username}/.config/gemini/.gemini_api_key) ${pkgs.gemini-cli}/bin/gemini --allowed-tools all --yolo --include-directories /Users/${username}/Downloads/Sidebery/ --include-directories /Users/${username}/dev/personal/notes/ "${prompt}"
+      #   GEMINI_API_KEY=$(cat /Users/${username}/.config/gemini/.gemini_api_key) ${pkgs.antigravity-cli}/bin/agy --allowed-tools all --yolo --include-directories /Users/${username}/Downloads/Sidebery/ --include-directories /Users/${username}/dev/personal/notes/ "${prompt}"
       # '';
       script = ''
-        GEMINI_API_KEY=$(cat /Users/${username}/.config/gemini/.gemini_api_key) ${pkgs.gemini-cli}/bin/gemini --allowed-tools all --yolo --include-directories "/Users/${username}/Downloads/firefox-history/,/Users/${username}/dev/personal/notes/" "${prompt} | tee -a /Users/${username}/dev/personal/gemini-archive/daily-summary-logs/$(date +"%Y-%m-%d").log"
+        GEMINI_API_KEY=$(cat /Users/${username}/.config/gemini/.gemini_api_key) ${pkgs.antigravity-cli}/bin/agy --allowed-tools all --yolo --include-directories "/Users/${username}/Downloads/firefox-history/,/Users/${username}/dev/personal/notes/" "${prompt} | tee -a /Users/${username}/dev/personal/gemini-archive/daily-summary-logs/$(date +"%Y-%m-%d").log"
       '';
 
       path = [