harden install script and fix fish config portability

Install script:
- fix package availability (skim/fedora, fd-find/debian, direnv+goku/macos)
- add CLI flags for non-interactive mode (--skip-timezone, --skip-neovim-bootstrap, etc.)
- template STEPS count per OS for correct TUI layout
- add brew shellenv for fresh Apple Silicon, timeout portability
- pam_ssh_agent_auth availability check with warning for Fedora 42+
- fix fisher detection, authorized_keys whole-line dedup

Fish config:
- replace set -gx PATH with idempotent fish_add_path
- guard direnv/cargo sourcing for missing tools
- fix hardcoded /home/anton/ and /Users/anton/ paths
- remove unused micromamba/conda setup

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

private_dot_config/private_fish/config.fish

@@ -1,12 +1,12 @@
-set -gx PATH /usr/local/opt/coreutils/libexec/gnubin $PATH
+fish_add_path /opt/homebrew/bin
-set -gx PATH /opt/homebrew/coreutils/libexec/gnubin $PATH
+fish_add_path /opt/homebrew/coreutils/libexec/gnubin
-set -gx PATH /opt/homebrew/bin $PATH
+fish_add_path /usr/local/opt/coreutils/libexec/gnubin
-set -gx PATH /usr/local/bin $PATH
+fish_add_path /usr/local/bin
-set -gx PATH /snap/bin $PATH
+fish_add_path /snap/bin
+fish_add_path $HOME/.local/bin
+fish_add_path $HOME/.cargo/bin
+fish_add_path $HOME/.go/bin
 set -gx GOPATH $HOME/.go
-set -gx PATH $HOME/.local/bin $PATH
-set -gx PATH $HOME/.cargo/bin $PATH
-set -gx PATH $HOME/.go/bin $PATH
 set -gx EDITOR nvim
 set fish_color_valid_path
 set -g fish_greeting
@@ -73,23 +73,9 @@ function winbox
 	~/dev/winbox/run.sh&
 end
 
-function conda
-	micromamba $argv
-end
 
-
+if test -e $HOME/.nix-profile/etc/profile.d/nix.fish
-
+    source $HOME/.nix-profile/etc/profile.d/nix.fish
-if [ -e /opt/homebrew/bin/micromamba ]
-	# >>> mamba initialize >>>
-	# !! Contents within this block are managed by 'mamba init' !!
-	set -gx MAMBA_EXE "/opt/homebrew/bin/micromamba"
-	set -gx MAMBA_ROOT_PREFIX "/Users/anton/micromamba"
-	$MAMBA_EXE shell hook --shell fish --root-prefix $MAMBA_ROOT_PREFIX | source
-	# <<< mamba initialize <<<
-end
-
-if [ -e /home/anton/.nix-profile/etc/profile.d/nix.fish ]; 
-	source /home/anton/.nix-profile/etc/profile.d/nix.fish; 
 end
 
 # The next line updates PATH for the Google Cloud SDK.
@@ -98,7 +84,9 @@ if [ -f ~/dev/google-cloud-sdk/path.fish.inc ]
 end
 
 
-direnv hook fish | source
+if type -q direnv
+    direnv hook fish | source
+end
 if [ -f ~/.config/op/plugins.sh ]
 	source ~/.config/op/plugins.sh 
 end
@@ -106,14 +94,16 @@ end
 #fish_vi_key_bindings
 
 # bun
-set --export BUN_INSTALL "$HOME/.bun"
+set -gx BUN_INSTALL "$HOME/.bun"
-set --export PATH $BUN_INSTALL/bin $PATH
+fish_add_path $HOME/.bun/bin
-source "$HOME/.cargo/env.fish"
+if test -f "$HOME/.cargo/env.fish"
+    source "$HOME/.cargo/env.fish"
+end
 
-export PATH="$PATH:/Users/anton/dev/screenpipe/target/debug"
+fish_add_path $HOME/dev/screenpipe/target/debug
 
 # Added by LM Studio CLI (lms)
-set -gx PATH $PATH /Users/anton/.cache/lm-studio/bin
+fish_add_path $HOME/.cache/lm-studio/bin
 
 # Added by OrbStack: command-line tools and integration
 # This won't be added again if you remove it.

run_onchange_after_install_main_deps.sh.tmpl

@@ -17,12 +17,46 @@
 
 
 #Config
+{{ if eq .chezmoi.os "darwin" -}}
+STEPS=9
+{{ else if eq .chezmoi.os "freebsd" -}}
+STEPS=9
+{{ else if eq .chezmoi.osRelease.id "ubuntu" -}}
 STEPS=14
+{{ else if eq .chezmoi.osRelease.id "debian" -}}
+STEPS=13
+{{ else -}}
+STEPS=12
+{{ end -}}
 PAD_LEN=4
 
 BASE_PACKAGES="gnupg curl wget git"
 ACT_PACKAGES="ripgrep unzip htop fzf bat gawk jq nnn tmux mc nethogs ngrep mtr gcc"
 
+# Non-interactive mode flags
+ASSUME_YES=0
+NON_INTERACTIVE=0
+SKIP_TIMEZONE=0
+SKIP_AUTH_KEYS=0
+SKIP_SHELL_CHANGE=0
+SKIP_NVIM_BOOTSTRAP=0
+
+while [ $# -gt 0 ]; do
+  case "$1" in
+    --yes) ASSUME_YES=1 ;;
+    --non-interactive) NON_INTERACTIVE=1 ;;
+    --skip-timezone) SKIP_TIMEZONE=1 ;;
+    --skip-authorized-keys) SKIP_AUTH_KEYS=1 ;;
+    --skip-shell-change) SKIP_SHELL_CHANGE=1 ;;
+    --skip-neovim-bootstrap) SKIP_NVIM_BOOTSTRAP=1 ;;
+    *) echo "Unknown option: $1"; exit 2 ;;
+  esac
+  shift
+done
+
+# Timeout portability (macOS has gtimeout via coreutils, not timeout)
+TIMEOUT_BIN="$(command -v timeout || command -v gtimeout || true)"
+
 #Colors
 Green='\033[0;32m'        # Green
 Blue='\033[0;34m'        # Blue
@@ -55,7 +89,8 @@ read
 
 
 #Setup
-TERM_WIDTH_BASE=$(stty size|awk '{print $2}')
+TERM_WIDTH_BASE=$(stty size 2>/dev/null | awk '{print $2}')
+TERM_WIDTH_BASE=${TERM_WIDTH_BASE:-80}
 PADDING=$(printf "%${PAD_LEN}s") # 4 spaces of padding
 TERM_WIDTH=$(($TERM_WIDTH_BASE - $PAD_LEN))
 USER=$(whoami)
@@ -125,9 +160,14 @@ new_line "Update caches and upgrade packages"
 
 
 {{ else if eq .chezmoi.os "darwin" -}}
-    if ! type brew;	then
+    if ! command -v brew >/dev/null 2>&1; then
 	  bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" 2>&1|pad
 	fi
+    if [ -x /opt/homebrew/bin/brew ]; then
+      eval "$(/opt/homebrew/bin/brew shellenv)"
+    elif [ -x /usr/local/bin/brew ]; then
+      eval "$(/usr/local/bin/brew shellenv)"
+    fi
     brew update 2>&1|pad
 
 {{ else if eq .chezmoi.osRelease.id "fedora" "almalinux" "rocky" -}}
@@ -150,7 +190,7 @@ new_line "Install base packages"
   sudo pkg install --yes $BASE_PACKAGES py39-pipx direnv 2>&1|pad
 
 {{ else if eq .chezmoi.os "darwin" -}}
-  brew install -q $BASE_PACKAGES python pipx 2>&1|pad
+  brew install -q $BASE_PACKAGES python pipx direnv goku 2>&1|pad
 
 {{ else if eq .chezmoi.osRelease.id "fedora" -}}
     sudo dnf install $BASE_PACKAGES direnv kitty-terminfo util-linux-user pipx -y 2>&1|pad
@@ -221,12 +261,24 @@ sudo pkg install --yes $ACT_PACKAGES neovim fish atuin lazygit fd-find pam_ssh_a
     brew install -q fish neovim $ACT_PACKAGES atuin jump fd sk dust lazygit 2>&1|pad
 
 {{ else if eq .chezmoi.osRelease.id "fedora"  -}}
-    sudo dnf install neovim fish $ACT_PACKAGES fd-find skim pam_ssh_agent_auth -y  2>&1|pad
+    PAM_SSH_PKG=""
+    if dnf list --quiet pam_ssh_agent_auth >/dev/null 2>&1; then
+      PAM_SSH_PKG="pam_ssh_agent_auth"
+    else
+      echo -e "${Yello}WARNING: pam_ssh_agent_auth not available in repos. sudo via SSH agent won't work.${NC}"
+    fi
+    sudo dnf install neovim fish $ACT_PACKAGES fd-find ${PAM_SSH_PKG:+$PAM_SSH_PKG} -y  2>&1|pad
 new_line "via NIX"
-	nix-env -iA nixpkgs.atuin nixpkgs.jump nixpkgs.du-dust nixpkgs.lazygit 2>&1|pad
+	nix-env -iA nixpkgs.atuin nixpkgs.jump nixpkgs.du-dust nixpkgs.lazygit nixpkgs.skim 2>&1|pad
 
 {{ else if eq .chezmoi.osRelease.id "almalinux" "rocky"  -}}
-    sudo dnf install neovim fish $ACT_PACKAGES fd-find pam_ssh_agent_auth -y  2>&1|pad
+    PAM_SSH_PKG=""
+    if dnf list --quiet pam_ssh_agent_auth >/dev/null 2>&1; then
+      PAM_SSH_PKG="pam_ssh_agent_auth"
+    else
+      echo -e "${Yello}WARNING: pam_ssh_agent_auth not available in repos. sudo via SSH agent won't work.${NC}"
+    fi
+    sudo dnf install neovim fish $ACT_PACKAGES fd-find ${PAM_SSH_PKG:+$PAM_SSH_PKG} -y  2>&1|pad
 new_line "via NIX"
 	nix-env -iA nixpkgs.fish nixpkgs.neovim nixpkgs.direnv nixpkgs.atuin nixpkgs.jump nixpkgs.du-dust nixpkgs.lazygit 2>&1|pad
 
@@ -238,7 +290,7 @@ new_line "via NIX"
 {{ else if eq .chezmoi.osRelease.id "debian" "ubuntu" -}}
     sudo apt-get install fish -y 2>&1|pad
 	sudo apt-get install neovim -y 2>&1|pad
-	sudo apt-get install $ACT_PACKAGES libpam-ssh-agent-auth -y 2>&1|pad
+	sudo apt-get install $ACT_PACKAGES fd-find libpam-ssh-agent-auth -y 2>&1|pad
 
 new_line "via NIX"
 	nix-env -iA nixpkgs.neovim nixpkgs.lazygit nixpkgs.jump nixpkgs.skim nixpkgs.du-dust nixpkgs.atuin 2>&1|pad
@@ -251,18 +303,22 @@ mkdir ~/.ssh 2>/dev/null || true
 cp ~/.ssh/authorized_keys ~/.ssh/authorized_keys.old 2>/dev/null || true
 
 ##print only unique lines
-cat ~/.ssh/authorized_keys.old <(echo "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIPdqIDeRKDOh7NQDcqnmLH/6M0ys7Wt/SEnF6ZYqroiH") 2>/dev/null | awk '!seen[$1]++' > ~/.ssh/authorized_keys
+cat ~/.ssh/authorized_keys.old <(echo "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIPdqIDeRKDOh7NQDcqnmLH/6M0ys7Wt/SEnF6ZYqroiH") 2>/dev/null | awk 'NF && !seen[$0]++' > ~/.ssh/authorized_keys
 
+if [ "$SKIP_NVIM_BOOTSTRAP" -eq 0 ]; then
 new_line "Waiting for neovim plugins and lsm compilations..."
-timeout 60s nvim --headless -c "sleep 1" -c ":Lazy! sync" -c "sleep 10" -c "qa" 2>&1|pad
+${TIMEOUT_BIN:+$TIMEOUT_BIN 60s} nvim --headless -c "sleep 1" -c ":Lazy! sync" -c "sleep 10" -c "qa" 2>&1|pad
-timeout 60s nvim --headless -c "sleep 1" -c ":MasonUpdate" -c "sleep 5" -c "qa" 2>&1|pad
+${TIMEOUT_BIN:+$TIMEOUT_BIN 60s} nvim --headless -c "sleep 1" -c ":MasonUpdate" -c "sleep 5" -c "qa" 2>&1|pad
-timeout 60s nvim --headless -c "sleep 1" -c ":MasonInstall lua-language-server" -c "sleep 5" -c "qa" 2>&1|pad
+${TIMEOUT_BIN:+$TIMEOUT_BIN 60s} nvim --headless -c "sleep 1" -c ":MasonInstall lua-language-server" -c "sleep 5" -c "qa" 2>&1|pad
-timeout 60s nvim --headless -c "sleep 1" -c ":MasonInstall rust-analyzer" -c "sleep 5" -c "qa" 2>&1|pad
+${TIMEOUT_BIN:+$TIMEOUT_BIN 60s} nvim --headless -c "sleep 1" -c ":MasonInstall rust-analyzer" -c "sleep 5" -c "qa" 2>&1|pad
-timeout 60s nvim --headless -c "sleep 1" -c ":TSUpdate" -c "sleep 5" -c "qa" 2>&1|pad
+${TIMEOUT_BIN:+$TIMEOUT_BIN 60s} nvim --headless -c "sleep 1" -c ":TSUpdate" -c "sleep 5" -c "qa" 2>&1|pad
+fi
 
 {{ if eq .chezmoi.os "linux" -}}
+    if [ "$SKIP_TIMEZONE" -eq 0 ]; then
       new_line "Setting timezone to Moscow"
       sudo timedatectl set-timezone Europe/Moscow
+    fi
 {{ end -}}
 
 new_line "Installing shell-gpt"
@@ -270,7 +326,7 @@ pipx install shell-gpt  2>&1|pad
 
 new_line "Install fisher plugin manager for fish"
 ## Install fisher plugin manager for fish, so that we may update in after plugin list sync by chezmoi
-if ! fish -c fisher &>/dev/null
+if ! fish -c "type -q fisher" &>/dev/null
 then
   fish -c "curl -sL https://raw.githubusercontent.com/jorgebucaran/fisher/main/functions/fisher.fish | source && fisher update" 2>&1|pad
 fi