Add shell module and bootstrap fixes

hosts/nanuqsaurus.nix

@@ -5,6 +5,7 @@
     inputs.lix-module.nixosModules.lixFromNixpkgs
     ../modules/system/base.nix
     ../modules/system/packages.nix
+    ../modules/system/shell.nix
     ../modules/system/home-manager-skel.nix
     ../modules/desktop/gnome-minimal.nix
     ../modules/users/admin.nix

modules/system/packages.nix

@@ -3,6 +3,7 @@
 {
   # Baseline system tools available everywhere; users run Home Manager standalone.
   config.environment.systemPackages = lib.mkAfter [
+    pkgs.git
     pkgs.ghostty
     pkgs.home-manager
     pkgs.just

modules/system/shell.nix

@@ -0,0 +1,39 @@
+{ pkgs, ... }:
+
+let
+  shellInitScript =
+    builtins.replaceStrings
+      [ "@ATUIN@" "@STARSHIP@" "@BASHPREEXEC@" ]
+      [
+        "${pkgs.atuin}/bin/atuin"
+        "${pkgs.starship}/bin/starship"
+        "${pkgs.bash-preexec}/share/bash/bash-preexec.sh"
+      ]
+      (builtins.readFile ../../scripts/shell-init.sh);
+in
+{
+
+  environment.systemPackages = [
+    pkgs.atuin
+    pkgs.bat
+    pkgs.eza
+    pkgs.fzf
+    pkgs.starship
+    pkgs.ugrep
+    pkgs.zoxide
+  ];
+
+  # Use Ghostty as the default terminal emulator.
+  environment.sessionVariables = {
+    TERMINAL = "${pkgs.ghostty}/bin/ghostty";
+    DEFAULT_TERMINAL = "${pkgs.ghostty}/bin/ghostty";
+  };
+
+  programs.bash = {
+    enable = true;
+    interactiveShellInit = shellInitScript;
+    loginShellInit = shellInitScript;
+    promptInit = ""; # avoid overriding Starship prompt
+  };
+  
+}

scripts/shell-init.sh

@@ -0,0 +1,155 @@
+log_shell_init() {
+  printf '%s\n' "shell-init: $*" >>/tmp/shell-init.log 2>/dev/null
+}
+
+ensure_bash_preexec() {
+  # Load bash-preexec to wire preexec/precmd hooks for Atuin.
+  if [ -n "${BASH_VERSION:-}" ] && [ -z "${bash_preexec_imported:-}" ] && [ -r "@BASHPREEXEC@" ]; then
+    # shellcheck disable=SC1090
+    . "@BASHPREEXEC@"
+    log_shell_init "bash-preexec sourced"
+  fi
+}
+
+append_prompt_command() {
+  local cmd="$1"
+  case ";${PROMPT_COMMAND:-};" in
+    *";$cmd;"*) log_shell_init "PROMPT_COMMAND already has $cmd" ;;
+    "")
+      PROMPT_COMMAND="$cmd"
+      log_shell_init "PROMPT_COMMAND set to $cmd"
+      ;;
+    *)
+      PROMPT_COMMAND="${PROMPT_COMMAND%;};$cmd"
+      log_shell_init "PROMPT_COMMAND appended $cmd -> ${PROMPT_COMMAND}"
+      ;;
+  esac
+}
+
+# Consider shells with a TTY interactive even if PS1 is empty.
+interactive=0
+if [ -t 1 ]; then
+  interactive=1
+elif [ -n "$PS1" ]; then
+  interactive=1
+fi
+
+# Ensure a sane TERM for prompt tools.
+if [ -z "${TERM:-}" ] || [ "$TERM" = "dumb" ]; then
+  export TERM=xterm-256color
+fi
+
+log_shell_init "TERM=$TERM PS1=${PS1:-<empty>} SHELL=$SHELL interactive=$interactive"
+
+# Ensure PS1 is set so Atuin/Starship init blocks run consistently.
+if [ $interactive -eq 1 ] && [ -z "${PS1:-}" ]; then
+  PS1='\\s-\\v\\$ '
+fi
+
+# Load bash-preexec early (needed by Atuin).
+if [ $interactive -eq 1 ]; then
+  ensure_bash_preexec
+  if command -v __bp_install >/dev/null 2>&1; then
+    __bp_install
+  fi
+fi
+
+# Prompt via Starship (manual init to avoid PROMPT_COMMAND being lost).
+if [ $interactive -eq 1 ] && command -v @STARSHIP@ >/dev/null 2>&1; then
+  log_shell_init "starship init"
+  case "$SHELL" in
+    */bash) eval "$(@STARSHIP@ init bash)" ;;
+    */zsh)  eval "$(@STARSHIP@ init zsh)" ;;
+  esac
+  append_prompt_command starship_precmd
+else
+  log_shell_init "starship skipped (not interactive or missing)"
+fi
+
+# Enable Atuin history integration after Starship so preexec/precmd arrays keep Atuin.
+if [ $interactive -eq 1 ] && command -v @ATUIN@ >/dev/null 2>&1; then
+  # Ensure session is established even if init script fails to export.
+  if [ -z "${ATUIN_SESSION:-}" ]; then
+    ATUIN_SESSION=$(@ATUIN@ uuid)
+    export ATUIN_SESSION
+    ATUIN_HISTORY_ID=""
+  fi
+  log_shell_init "atuin init"
+  case "$SHELL" in
+    */bash) eval "$(@ATUIN@ init bash)" ;;
+    */zsh)  eval "$(@ATUIN@ init zsh)" ;;
+  esac
+  # Ensure Atuin hooks stay present.
+  if [ -n "${preexec_functions[*]:-}" ]; then
+    # Remove existing duplicates then prepend Atuin.
+    tmp=()
+    for f in "${preexec_functions[@]}"; do
+      [ "$f" = "__atuin_preexec" ] && continue
+      tmp+=("$f")
+    done
+    preexec_functions=(__atuin_preexec "${tmp[@]}")
+    unset tmp
+  else
+    preexec_functions=(__atuin_preexec)
+  fi
+  if [ -n "${precmd_functions[*]:-}" ]; then
+    tmp=()
+    for f in "${precmd_functions[@]}"; do
+      [ "$f" = "__atuin_precmd" ] && continue
+      tmp+=("$f")
+    done
+    precmd_functions=(__atuin_precmd "${tmp[@]}")
+    unset tmp
+  else
+    precmd_functions=(__atuin_precmd)
+  fi
+else
+  log_shell_init "atuin skipped"
+fi
+
+# Directory jumping via zoxide.
+if [ $interactive -eq 1 ] && command -v zoxide >/dev/null 2>&1; then
+  log_shell_init "zoxide init"
+  case "$SHELL" in
+    */bash) eval "$(zoxide init bash)" ;;
+    */zsh)  eval "$(zoxide init zsh)" ;;
+  esac
+else
+  log_shell_init "zoxide skipped"
+fi
+
+# Ensure zoxide hook stays in PROMPT_COMMAND even if starship overwrote it.
+if [ $interactive -eq 1 ] && command -v __zoxide_hook >/dev/null 2>&1; then
+  append_prompt_command __zoxide_hook
+fi
+
+# Ensure bash-preexec precmd is present even if other init overwrote PROMPT_COMMAND.
+if [ $interactive -eq 1 ] && command -v __bp_precmd_invoke_cmd >/dev/null 2>&1; then
+  append_prompt_command __bp_precmd_invoke_cmd
+fi
+if [ $interactive -eq 1 ] && command -v __bp_interactive_mode >/dev/null 2>&1; then
+  append_prompt_command __bp_interactive_mode
+fi
+
+# ls aliases via eza.
+if command -v eza >/dev/null 2>&1; then
+  alias ll='eza -l --icons=auto --group-directories-first'
+  alias l.='eza -d .*'
+  alias ls='eza'
+  alias l1='eza -1'
+fi
+
+# grep aliases via ugrep.
+if command -v ug >/dev/null 2>&1; then
+  alias grep='ug'
+  alias egrep='ug -E'
+  alias fgrep='ug -F'
+  alias xzgrep='ug -z'
+  alias xzegrep='ug -zE'
+  alias xzfgrep='ug -zF'
+fi
+
+# bat for cat.
+if command -v bat >/dev/null 2>&1; then
+  alias cat='bat --style=plain --pager=never' 2>/dev/null
+fi

templates/home-home.nix

@@ -70,7 +70,12 @@
     '';
   };
 
-  home.sessionVariables = { };
+  home.sessionVariables = {
+    # you can change the default terminal and editor here
+    TERMINAL = "${pkgs.ghostty}/bin/ghostty";
+    DEFAULT_TERMINAL = "${pkgs.ghostty}/bin/ghostty";
+    EDITOR = "${pkgs.micro}/bin/micro";
+  };
 
   programs.home-manager.enable = true;
 }