From 930d15c906bb11800d56357af8a5f12c16211190 Mon Sep 17 00:00:00 2001
From: cmargalejo <cristinamargalejoblasco@gmail.com>
Date: Tue, 7 Apr 2026 10:59:14 +0200
Subject: [PATCH 1/9] Add interactive installation script and README

---
 scripts/installation/README.md       |  74 ++++
 scripts/installation/install_rest.sh | 551 +++++++++++++++++++++++++++
 2 files changed, 625 insertions(+)
 create mode 100644 scripts/installation/README.md
 create mode 100644 scripts/installation/install_rest.sh

diff --git a/scripts/installation/README.md b/scripts/installation/README.md
new file mode 100644
index 000000000..310ca1633
--- /dev/null
+++ b/scripts/installation/README.md
@@ -0,0 +1,74 @@
+# Installation Scripts
+
+Interactive installer for [REST-for-Physics](https://github.com/rest-for-physics/framework) and its dependencies.
+
+## Quick start
+
+```bash
+bash install_rest.sh
+```
+
+The script is interactive and will guide you through each step.
+
+## Install modes
+
+### Mode 1 -- Server install
+
+For machines where ROOT, Geant4 and Garfield++ are already available system-wide
+(e.g. the `titan` cluster at Zaragoza).
+
+You will be asked for the path to the system `thisREST.sh` that loads the
+pre-installed environment. The script then clones, configures and builds only
+REST itself.
+
+### Mode 2 -- Full install from source
+
+For a fresh Ubuntu (22.04/24.04) or WSL system with nothing pre-installed.
+Builds everything from source:
+
+| Package       | Version                          |
+|---------------|----------------------------------|
+| ROOT          | 6.26.10                          |
+| Geant4        | 11.0.3 (with GDML + data)       |
+| Garfield++    | pinned commit `a993c5eb`         |
+| REST          | latest from `master`             |
+
+System dependencies are installed via `apt` (requires `sudo`).
+If `sudo` is not available the script offers to skip this step, assuming
+packages are already present.
+
+## What the script does
+
+1. Installs system packages (mode 2, optional)
+2. Downloads and builds ROOT, Geant4, Garfield++ (mode 2)
+3. Asks you to choose which REST libraries to enable
+4. Clones the REST framework and pulls submodules
+5. Configures and builds REST with CMake
+6. Tests the installation (`restRoot`)
+7. Optionally adds the environment setup to `~/.bashrc`
+
+## Options asked during installation
+
+- **Install directory** -- where REST source and build will live (default: `~/rest`)
+- **Libraries** -- all, a common subset, or pick individually
+- **Garfield++ / Geant4 integration** -- enable or disable
+- **Submodule strategy** -- latest commits or framework-pinned versions
+- **Parallel jobs** -- capped at 16 for shared-server politeness
+
+## Individual scripts (legacy)
+
+The older per-package scripts are still available for reference:
+
+- `installROOT.sh` -- ROOT 6.28.02
+- `installGeant4.sh` -- Geant4 11.0.3
+- `installGarfield.sh` -- Garfield++
+- `installRequiredSoftware.sh` -- system packages via `apt-get`
+
+`install_rest.sh` supersedes all of them in a single guided workflow.
+
+## Requirements
+
+- **OS**: Ubuntu 22.04 / 24.04 (or WSL with either). Other Linux distros may
+  work but the `apt` package list would need adapting.
+- **Disk**: ~5 GB for a full build (ROOT + Geant4 + Garfield + REST)
+- **Tools**: `bash`, `git`, `python3`, `cmake`, `make`, `wget`
diff --git a/scripts/installation/install_rest.sh b/scripts/installation/install_rest.sh
new file mode 100644
index 000000000..7d67c1d8b
--- /dev/null
+++ b/scripts/installation/install_rest.sh
@@ -0,0 +1,551 @@
+#!/bin/bash
+# =============================================================================
+#  REST-for-Physics -- Interactive Installation Script
+#  https://github.com/rest-for-physics/framework
+#
+#  Supports two modes:
+#    1. Server install  -- ROOT/Geant4/Garfield already available (e.g. titan)
+#    2. Full install    -- Builds ROOT 6.26.10, Geant4 11.0.3, Garfield++, REST
+#                         from source (e.g. WSL / fresh Ubuntu)
+#
+#  Usage:  bash install_rest.sh
+# =============================================================================
+
+# Self-fix Windows line endings before anything else
+grep -q $'\r' "$0" 2>/dev/null && sed -i 's/\r//' "$0" && exec bash "$0" "$@"
+
+set -euo pipefail
+
+# -- Colours ------------------------------------------------------------------
+RED='\033[0;31m'; GREEN='\033[0;32m'; YELLOW='\033[1;33m'
+CYAN='\033[0;36m'; BOLD='\033[1m'; RESET='\033[0m'
+
+info()    { echo -e "${CYAN}[INFO]${RESET}  $*"; }
+success() { echo -e "${GREEN}[OK]${RESET}    $*"; }
+warn()    { echo -e "${YELLOW}[WARN]${RESET}  $*"; }
+error()   { echo -e "${RED}[ERROR]${RESET} $*"; exit 1; }
+ask()     { echo -e "${BOLD}$*${RESET}"; }
+sep()     { echo "-------------------------------------------------------------"; }
+
+# -- Banner -------------------------------------------------------------------
+echo -e "${CYAN}"
+echo "  ____  _____ ____ _____      ___                 ____  _               _"
+echo " |  _ \| ____/ ___|_   _|    / _| ___  _ __      |  _ \| |__  _   _ ___(_) ___ ___"
+echo " | |_) |  _| \___ \ | |     | |_ / _ \| '__|     | |_) | '_ \| | | / __| |/ __/ __|"
+echo " |  _ <| |___ ___) || |     |  _| (_) | |        |  __/| | | | |_| \__ \ | (__\__ \\"
+echo " |_| \_\_____|____/ |_|     |_|  \___/|_|        |_|   |_| |_|\__, |___/_|\___|___/"
+echo "                                                                |___/"
+echo -e "${RESET}"
+echo "  REST-for-Physics installation script"
+echo "  https://github.com/rest-for-physics/framework"
+echo ""
+
+# -- GCC compatibility flags (fixes GCC 14 -Werror issues) --------------------
+GCC_COMPAT_FLAGS="-Wno-error=ignored-attributes -Wno-error=overloaded-virtual -Wno-error=maybe-uninitialized"
+
+# =============================================================================
+#  STEP 0 -- Choose install mode
+# =============================================================================
+sep
+ask "Choose installation mode:"
+echo "  1) Server install  -- use pre-installed ROOT/Geant4/Garfield on this machine"
+echo "     (for clusters like titan where a system REST environment exists)"
+echo "  2) Full install    -- build ROOT, Geant4, Garfield++ and REST from source"
+echo "     (for a fresh Ubuntu / WSL system)"
+echo ""
+read -rp "Enter choice [1/2]: " INSTALL_MODE
+
+case "$INSTALL_MODE" in
+    1) info "Mode: Server install (using pre-built dependencies)" ;;
+    2) info "Mode: Full install from source" ;;
+    *) error "Invalid choice. Please run again and enter 1 or 2." ;;
+esac
+echo ""
+
+# =============================================================================
+#  STEP 1 -- Choose install directory
+# =============================================================================
+sep
+DEFAULT_DIR="$HOME/rest"
+ask "Where do you want to install REST?"
+read -rp "Install directory [default: $DEFAULT_DIR]: " REST_DIR
+REST_DIR="${REST_DIR:-$DEFAULT_DIR}"
+REST_DIR="${REST_DIR/#\~/$HOME}"   # expand ~ manually
+info "REST will be installed in: $REST_DIR"
+echo ""
+
+if [[ -d "$REST_DIR" ]]; then
+    warn "Directory $REST_DIR already exists."
+    read -rp "Continue and use it anyway? [y/N]: " CONFIRM
+    [[ "$CONFIRM" =~ ^[Yy]$ ]] || error "Aborted."
+fi
+
+# =============================================================================
+#  MODE 2 -- Full install: check/install system dependencies
+# =============================================================================
+if [[ "$INSTALL_MODE" == "2" ]]; then
+
+    sep
+    # Check for sudo access before attempting anything
+    SKIP_APT=false
+    if ! sudo -v 2>/dev/null; then
+        warn "Cannot obtain sudo access."
+        warn "If system packages are already installed, you can skip this step."
+        read -rp "Skip apt package installation? [y/N]: " SKIP_APT_ANS
+        if [[ "$SKIP_APT_ANS" =~ ^[Yy]$ ]]; then
+            SKIP_APT=true
+            info "Skipping apt package installation."
+        else
+            error "Mode 2 requires sudo access to install system packages.\n       On shared servers (e.g. titan), use mode 1 instead."
+        fi
+    fi
+
+    if [[ "$SKIP_APT" == false ]]; then
+        warn "This package list was designed for Ubuntu 22/24 with ROOT 6.26.10,"
+        warn "Geant4 11.0.3 and Garfield++. It has not been fully tested on a"
+        warn "fresh system yet. If something fails, a package may be missing or"
+        warn "named differently on your Ubuntu version."
+        read -rp "Press Enter to continue or Ctrl+C to abort: "
+        echo ""
+        info "Installing system dependencies (requires sudo)..."
+        sudo apt update && sudo apt install -y \
+            build-essential cmake git wget curl \
+            gcc-11 g++-11 gfortran \
+            python3 python3-full python3-pip python3-numpy \
+            libssl-dev libxerces-c-dev libxml2-dev \
+            nlohmann-json3-dev \
+            libxxhash-dev libzstd-dev liblzma-dev liblz4-dev \
+            libfreetype6-dev \
+            libglew-dev libgl2ps-dev \
+            libx11-dev libxpm-dev libxft-dev libxext-dev \
+            libxmu-dev libxi-dev \
+            libgl1-mesa-dev libglu1-mesa-dev freeglut3-dev mesa-common-dev \
+            qtbase5-dev qtchooser qt5-qmake qtbase5-dev-tools \
+            libfftw3-dev libtinyxml2-dev libgsl-dev libglpk-dev \
+            libcfitsio-dev libcurl4-openssl-dev \
+            software-properties-common
+
+        # Python 3.10 for ROOT 6.26 compatibility
+        info "Adding deadsnakes PPA and installing Python 3.10..."
+        sudo add-apt-repository ppa:deadsnakes/ppa -y
+        sudo apt update
+        sudo apt install -y python3.10 python3.10-dev python3.10-venv
+        success "System dependencies installed."
+    fi
+    echo ""
+
+    SOFTWARE_DIR="$REST_DIR/../software"
+    SOFTWARE_DIR="$(realpath -m "$SOFTWARE_DIR")"
+    mkdir -p "$SOFTWARE_DIR"
+    info "Dependencies will be built in: $SOFTWARE_DIR"
+
+    # -- ROOT 6.26.10 --------------------------------------------------------
+    sep
+    info "Downloading and building ROOT 6.26.10 (this takes a while)..."
+    cd "$SOFTWARE_DIR"
+    if [[ ! -f root_v6.26.10.source.tar.gz ]]; then
+        wget https://root.cern/download/root_v6.26.10.source.tar.gz
+    fi
+    if [[ ! -d root-6.26.10 ]]; then
+        tar xzf root_v6.26.10.source.tar.gz
+    else
+        info "ROOT source directory already exists, skipping extraction."
+    fi
+    cd root-6.26.10
+    mkdir -p root_build root_install
+    cd root_build
+    cmake .. \
+        -DCMAKE_INSTALL_PREFIX=../root_install \
+        -DPython3_EXECUTABLE=/usr/bin/python3.10 \
+        -DCMAKE_C_COMPILER=gcc-11 \
+        -DCMAKE_CXX_COMPILER=g++-11 \
+        -DCMAKE_CXX_STANDARD=17 \
+        -Dnetxng=OFF -Dxrootd=OFF
+    make -j"$(nproc)" install
+    ROOT_THISROOT="$SOFTWARE_DIR/root-6.26.10/root_install/bin/thisroot.sh"
+    set +u
+    source "$ROOT_THISROOT"
+    set -u
+    success "ROOT 6.26.10 installed."
+    echo ""
+
+    # -- Geant4 11.0.3 -------------------------------------------------------
+    sep
+    info "Downloading and building Geant4 11.0.3..."
+    cd "$SOFTWARE_DIR"
+    if [[ ! -f geant4-v11.0.3.tar.gz ]]; then
+        wget https://gitlab.cern.ch/geant4/geant4/-/archive/v11.0.3/geant4-v11.0.3.tar.gz
+    fi
+    if [[ ! -d geant4-v11.0.3 ]]; then
+        tar xzf geant4-v11.0.3.tar.gz
+    else
+        info "Geant4 source directory already exists, skipping extraction."
+    fi
+    cd geant4-v11.0.3
+    mkdir -p build install
+    cd build
+    cmake .. \
+        -DCMAKE_INSTALL_PREFIX=../install \
+        -DGEANT4_INSTALL_DATA=ON \
+        -DGEANT4_USE_OPENGL_X11=ON \
+        -DGEANT4_BUILD_MULTITHREADED=ON \
+        -DCMAKE_C_COMPILER=gcc-11 \
+        -DCMAKE_CXX_COMPILER=g++-11 \
+        -DGEANT4_USE_GDML=ON
+    make -j"$(nproc)" install
+    # Fix ownership if files ended up root-owned (e.g. from a previous sudo run)
+    if [[ -O "$SOFTWARE_DIR/geant4-v11.0.3/install" ]]; then
+        : # Already owned by current user, nothing to do
+    else
+        sudo chown -R "$(whoami):$(whoami)" "$SOFTWARE_DIR/geant4-v11.0.3/install"
+    fi
+    GEANT4_SH="$SOFTWARE_DIR/geant4-v11.0.3/install/bin/geant4.sh"
+    set +u
+    source "$GEANT4_SH"
+    set -u
+    success "Geant4 11.0.3 installed."
+    echo ""
+
+    # -- Garfield++ ----------------------------------------------------------
+    sep
+    info "Cloning and building Garfield++ (pinned commit for REST compatibility)..."
+    cd "$SOFTWARE_DIR"
+    if [[ ! -d garfield ]]; then
+        git clone https://gitlab.cern.ch/garfield/garfieldpp.git garfield
+    fi
+    cd garfield
+    git checkout a993c5eb015e23aa4bccdd1bdda027314afc2153
+    mkdir -p build
+    cd build
+    cmake .. \
+        -DCMAKE_INSTALL_PREFIX=../install \
+        -DCMAKE_C_COMPILER=gcc-11 \
+        -DCMAKE_CXX_COMPILER=g++-11
+    make -j"$(nproc)" install
+    # Fix legacy HEED include paths
+    cp -r "$SOFTWARE_DIR/garfield/Heed" "$SOFTWARE_DIR/garfield/install/"
+    GARFIELD_SETUP="$SOFTWARE_DIR/garfield/install/share/Garfield/setupGarfield.sh"
+    success "Garfield++ installed."
+    echo ""
+
+fi  # end MODE 2 dependencies
+
+# =============================================================================
+#  STEP 2 -- Source the environment (mode 1: system; mode 2: freshly built)
+# =============================================================================
+sep
+
+if [[ "$INSTALL_MODE" == "1" ]]; then
+    ask "Enter the path to the system thisREST.sh to load ROOT/Geant4/Garfield:"
+    echo "  Example: /programas/titan/rest/latest/thisREST.sh"
+    read -rp "Path: " SYSTEM_THIS_REST
+    SYSTEM_THIS_REST="${SYSTEM_THIS_REST/#\~/$HOME}"
+    if [[ ! -f "$SYSTEM_THIS_REST" ]]; then
+        error "File not found: $SYSTEM_THIS_REST"
+    fi
+    info "Sourcing system environment: $SYSTEM_THIS_REST"
+    # shellcheck disable=SC1090
+    set +u
+    source "$SYSTEM_THIS_REST"
+    set -u
+    success "System environment loaded."
+else
+    # Already sourced above during build
+    set +u
+    source "$ROOT_THISROOT"
+    source "$GEANT4_SH"
+    source "$GARFIELD_SETUP"
+    set -u
+    success "Build environment loaded."
+fi
+echo ""
+
+# =============================================================================
+#  STEP 3 -- Choose libraries to enable
+# =============================================================================
+sep
+ask "Which REST libraries do you want to enable?"
+echo "  1) All libraries  (REST_ALL_LIBS=ON  -- recommended, includes everything)"
+echo "  2) Common subset  (detector + raw + track + Garfield + Geant4)"
+echo "  3) Custom         (you will be asked for each library)"
+echo ""
+read -rp "Enter choice [1/2/3, default: 1]: " LIB_CHOICE
+LIB_CHOICE="${LIB_CHOICE:-1}"
+
+case "$LIB_CHOICE" in
+    1)
+        CMAKE_LIB_FLAGS="-DREST_ALL_LIBS=ON"
+        ;;
+    2)
+        CMAKE_LIB_FLAGS="-DRESTLIB_DETECTOR=ON -DRESTLIB_RAW=ON -DRESTLIB_TRACK=ON"
+        ;;
+    3)
+        CMAKE_LIB_FLAGS=""
+        for LIB in AXION CONNECTORS DETECTOR GEANT4 LEGACY RAW TRACK WIMP; do
+            read -rp "  Enable RESTLIB_${LIB}? [y/N]: " LANS
+            [[ "$LANS" =~ ^[Yy]$ ]] && CMAKE_LIB_FLAGS="$CMAKE_LIB_FLAGS -DRESTLIB_${LIB}=ON"
+        done
+        ;;
+    *)
+        warn "Invalid choice, defaulting to all libraries."
+        CMAKE_LIB_FLAGS="-DREST_ALL_LIBS=ON"
+        ;;
+esac
+
+# Always ask about Garfield and Geant4 integrations
+echo ""
+read -rp "Enable Garfield++ integration? (REST_GARFIELD) [Y/n]: " GARF_ANS
+[[ ! "$GARF_ANS" =~ ^[Nn]$ ]] && CMAKE_LIB_FLAGS="$CMAKE_LIB_FLAGS -DREST_GARFIELD=ON"
+
+read -rp "Enable Geant4 integration / restG4? (REST_G4) [Y/n]: " G4_ANS
+[[ ! "$G4_ANS" =~ ^[Nn]$ ]] && CMAKE_LIB_FLAGS="$CMAKE_LIB_FLAGS -DREST_G4=ON"
+
+info "CMake library flags: $CMAKE_LIB_FLAGS"
+echo ""
+
+# =============================================================================
+#  STEP 4 -- Choose submodule update strategy
+# =============================================================================
+sep
+ask "How do you want to pull REST submodules?"
+echo "  1) --latest   Pull the latest commit from each submodule branch"
+echo "               (may occasionally be incompatible but stays up to date)"
+echo "  2) (default)  Use the version recorded in the framework repository"
+echo "               (safer, guaranteed compatible)"
+echo ""
+read -rp "Enter choice [1/2, default: 2]: " SUB_CHOICE
+SUB_CHOICE="${SUB_CHOICE:-2}"
+
+# =============================================================================
+#  STEP 5 -- Clone / update REST framework
+# =============================================================================
+sep
+if [[ -d "$REST_DIR/.git" ]]; then
+    info "REST repository already exists at $REST_DIR, updating..."
+    cd "$REST_DIR"
+    git pull
+else
+    info "Cloning REST framework into $REST_DIR..."
+    if [[ -d "$REST_DIR" && "$(ls -A "$REST_DIR" 2>/dev/null)" ]]; then
+        # Directory exists and is non-empty; clone to temp then move contents
+        TMPCLONE="$(mktemp -d)"
+        git clone https://github.com/rest-for-physics/framework.git "$TMPCLONE/framework"
+        shopt -s dotglob
+        mv "$TMPCLONE/framework"/* "$REST_DIR/"
+        shopt -u dotglob
+        rm -rf "$TMPCLONE"
+    else
+        git clone https://github.com/rest-for-physics/framework.git "$REST_DIR"
+    fi
+    cd "$REST_DIR"
+fi
+
+if ! command -v python3 &>/dev/null; then
+    error "python3 not found in PATH. Please install Python 3 and retry."
+fi
+
+info "Pulling submodules..."
+# --onlylibs skips private university repos (iaxo, detector-template, etc.)
+# that would hang waiting for SSH access most users don't have.
+# If REST_G4 is enabled, also pull the restG4 package explicitly.
+if [[ "$SUB_CHOICE" == "1" ]]; then
+    python3 "$REST_DIR/pull-submodules.py" --latest --onlylibs
+else
+    # --clean asks "Are you sure?" — answer automatically to avoid consuming
+    # the main script's stdin when running non-interactively.
+    echo y | python3 "$REST_DIR/pull-submodules.py" --clean --onlylibs
+fi
+
+# restG4 lives in packages/, not libraries/, so --onlylibs skips it.
+# Pull it explicitly if Geant4 integration was requested.
+if [[ "$CMAKE_LIB_FLAGS" == *"REST_G4=ON"* ]]; then
+    info "Pulling restG4 package..."
+    echo y | python3 "$REST_DIR/pull-submodules.py" --clean --only:restG4
+fi
+success "REST framework and submodules ready."
+echo ""
+
+# =============================================================================
+#  STEP 6 -- Configure and build
+# =============================================================================
+sep
+ask "How many parallel jobs for make? (be careful on shared servers)"
+NCPU=$(nproc 2>/dev/null || echo 4)
+if [[ "$NCPU" -gt 16 ]]; then
+    NCPU=8
+fi
+read -rp "Jobs [default: $NCPU, max: 16]: " NJOBS
+NJOBS="${NJOBS:-$NCPU}"
+if ! [[ "$NJOBS" =~ ^[0-9]+$ ]]; then
+    warn "Invalid number '$NJOBS', defaulting to $NCPU."
+    NJOBS="$NCPU"
+fi
+if [[ "$NJOBS" -gt 16 ]]; then
+    warn "Capping parallel jobs at 16 to be polite on shared servers."
+    NJOBS=16
+fi
+
+BUILD_DIR="$REST_DIR/build"
+INSTALL_DIR="$REST_DIR/install"
+
+mkdir -p "$BUILD_DIR"
+cd "$BUILD_DIR"
+
+# Clean stale CMakeCache if present
+if [[ -f CMakeCache.txt ]]; then
+    warn "Existing build directory found. Cleaning CMakeCache..."
+    rm -f CMakeCache.txt
+fi
+
+info "Running cmake..."
+
+# shellcheck disable=SC2086
+cmake "$REST_DIR" \
+    -DCMAKE_INSTALL_PREFIX="$INSTALL_DIR" \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DCMAKE_CXX_FLAGS="$GCC_COMPAT_FLAGS" \
+    $CMAKE_LIB_FLAGS
+
+echo ""
+info "Building REST with $NJOBS parallel jobs..."
+info "This can take 15-40 minutes on a first build."
+echo ""
+
+make -j"$NJOBS" install
+success "REST compiled and installed in $INSTALL_DIR"
+echo ""
+
+# =============================================================================
+#  STEP 7 -- Test
+# =============================================================================
+sep
+info "Testing installation..."
+set +u
+source "$INSTALL_DIR/thisREST.sh"
+set -u
+if command -v restRoot &>/dev/null; then
+    success "restRoot is available -- installation successful!"
+else
+    warn "restRoot not found in PATH. Check the output above for errors."
+fi
+echo ""
+
+# =============================================================================
+#  STEP 8 -- Optional: add to .bashrc
+# =============================================================================
+sep
+# Flush any leftover input from the build output before asking
+# Flush leftover keystrokes only when running interactively
+[[ -t 0 ]] && { read -r -t 0.1 -n 10000 discard 2>/dev/null || true; }
+ask "How do you want to set up your ~/.bashrc?"
+echo "  1) Full setup    -- system environment + your local REST"
+echo "                      (recommended for new users)"
+echo "  2) System only   -- only add the system thisREST.sh"
+echo "                      (you source your local REST manually when needed)"
+echo "  3) No            -- do not touch ~/.bashrc"
+echo ""
+read -rp "Enter choice [1/2/3, default: 1]: " BASHRC_CHOICE
+BASHRC_CHOICE="${BASHRC_CHOICE:-1}"
+
+case "$BASHRC_CHOICE" in
+    1|2)
+        if [[ "$BASHRC_CHOICE" == "1" ]]; then
+            # Full setup: system env + local REST
+            if [[ "$INSTALL_MODE" == "1" ]]; then
+                BASHRC_BLOCK="
+# -- REST-for-Physics ---------------------------------------------------------
+source \"$SYSTEM_THIS_REST\"   # loads system ROOT / Geant4 / Garfield
+source \"$INSTALL_DIR/thisREST.sh\"   # your local REST install
+# -----------------------------------------------------------------------------"
+            else
+                BASHRC_BLOCK="
+# -- REST-for-Physics ---------------------------------------------------------
+source \"$ROOT_THISROOT\"
+source \"$GEANT4_SH\"
+source \"$GARFIELD_SETUP\"
+source \"$INSTALL_DIR/thisREST.sh\"   # your local REST install
+# -----------------------------------------------------------------------------"
+            fi
+            CHECK_LINE="$INSTALL_DIR/thisREST.sh"
+        else
+            # System only
+            if [[ "$INSTALL_MODE" == "1" ]]; then
+                BASHRC_BLOCK="
+# -- REST-for-Physics ---------------------------------------------------------
+source \"$SYSTEM_THIS_REST\"   # loads system ROOT / Geant4 / Garfield
+# source \"$INSTALL_DIR/thisREST.sh\"   # uncomment to use your local REST build
+# -----------------------------------------------------------------------------"
+            else
+                BASHRC_BLOCK="
+# -- REST-for-Physics ---------------------------------------------------------
+source \"$ROOT_THISROOT\"
+source \"$GEANT4_SH\"
+source \"$GARFIELD_SETUP\"
+# source \"$INSTALL_DIR/thisREST.sh\"   # uncomment to use your local REST build
+# -----------------------------------------------------------------------------"
+            fi
+            CHECK_LINE="REST-for-Physics"
+            info "Your local REST is installed at: $INSTALL_DIR/thisREST.sh"
+            info "Source it manually any time you want to switch to your local build."
+        fi
+
+        # Avoid duplicate entries
+        if grep -qF "$CHECK_LINE" ~/.bashrc 2>/dev/null; then
+            warn "~/.bashrc already contains a REST entry -- skipping."
+        else
+            echo "$BASHRC_BLOCK" >> ~/.bashrc
+            success "Added to ~/.bashrc."
+        fi
+
+        # ROOT browser fix
+        if [[ ! -f "$HOME/.rootrc" ]]; then
+            echo "Browser.Name: TRootBrowser" > "$HOME/.rootrc"
+            info "Created ~/.rootrc with TRootBrowser fix."
+        fi
+        ;;
+    3)
+        info "~/.bashrc left unchanged."
+        info "To activate REST manually:"
+        if [[ "$INSTALL_MODE" == "1" ]]; then
+            info "  source $SYSTEM_THIS_REST"
+        fi
+        info "  source $INSTALL_DIR/thisREST.sh"
+        ;;
+    *)
+        warn "Invalid choice, ~/.bashrc left unchanged."
+        ;;
+esac
+echo ""
+
+# =============================================================================
+#  Done!
+# =============================================================================
+echo -e "${GREEN}${BOLD}"
+echo "  +------------------------------------------------------------+"
+echo "  |      REST-for-Physics installation complete!               |"
+echo "  +------------------------------------------------------------+"
+echo -e "${RESET}"
+echo "  To activate REST (if not already in your ~/.bashrc):"
+if [[ "$INSTALL_MODE" == "1" ]]; then
+    echo "    source $SYSTEM_THIS_REST   # system ROOT/Geant4/Garfield"
+fi
+echo "    source $INSTALL_DIR/thisREST.sh   # your local REST build"
+echo ""
+echo "  Quick test:    restRoot"
+echo "  Docs:          https://rest-for-physics.github.io"
+echo "  Forum:         https://rest-forum.unizar.es"
+echo ""
+echo -e "${BOLD}\033[0;35m"
+echo "  +------------------------------------------------------+"
+echo "  |                                                      |"
+echo "  |      Congratulations! You have survived the          |"
+echo "  |                 installation. :)                     |"
+echo "  |                                                      |"
+echo "  |      You are now ready to toil and suffer in         |"
+echo "  |               more interesting ways.                 |"
+echo "  |                                                      |"
+echo "  |          Welcome to REST-for-Physics!                |"
+echo "  |                                                      |"
+echo "  +------------------------------------------------------+"
+echo -e "${RESET}"
+echo ""
\ No newline at end of file

From 9df8f96fcd0ea3830cd189ce8b216e637c6f5c1c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 7 Apr 2026 09:30:19 +0000
Subject: [PATCH 2/9] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 scripts/installation/install_rest.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/installation/install_rest.sh b/scripts/installation/install_rest.sh
index 7d67c1d8b..4e1af0314 100644
--- a/scripts/installation/install_rest.sh
+++ b/scripts/installation/install_rest.sh
@@ -548,4 +548,4 @@ echo "  |          Welcome to REST-for-Physics!                |"
 echo "  |                                                      |"
 echo "  +------------------------------------------------------+"
 echo -e "${RESET}"
-echo ""
\ No newline at end of file
+echo ""

From 7729e4636ba75bc0d505ed0b07c41b3f9ab8396c Mon Sep 17 00:00:00 2001
From: cmargalejo <cristinamargalejoblasco@gmail.com>
Date: Mon, 13 Apr 2026 12:22:28 +0200
Subject: [PATCH 3/9] Including sultan path for REST and rewording of
 submodules choice

---
 scripts/installation/install_rest.sh | 29 ++++++++++++++++++++--------
 1 file changed, 21 insertions(+), 8 deletions(-)

diff --git a/scripts/installation/install_rest.sh b/scripts/installation/install_rest.sh
index 4e1af0314..73e39e8e5 100644
--- a/scripts/installation/install_rest.sh
+++ b/scripts/installation/install_rest.sh
@@ -237,8 +237,19 @@ sep
 
 if [[ "$INSTALL_MODE" == "1" ]]; then
     ask "Enter the path to the system thisREST.sh to load ROOT/Geant4/Garfield:"
-    echo "  Example: /programas/titan/rest/latest/thisREST.sh"
-    read -rp "Path: " SYSTEM_THIS_REST
+    echo "  Sultan: /programas/rest/latest/thisREST.sh"
+    echo "  Titan:  /programas/titan/rest/latest/thisREST.sh"
+    case "$(hostname)" in
+        *sultan*) DEFAULT_THIS_REST="/programas/rest/latest/thisREST.sh" ;;
+        *titan*)  DEFAULT_THIS_REST="/programas/titan/rest/latest/thisREST.sh" ;;
+        *)        DEFAULT_THIS_REST="" ;;
+    esac
+    if [[ -n "$DEFAULT_THIS_REST" ]]; then
+        read -rp "Path [default: $DEFAULT_THIS_REST]: " SYSTEM_THIS_REST
+        SYSTEM_THIS_REST="${SYSTEM_THIS_REST:-$DEFAULT_THIS_REST}"
+    else
+        read -rp "Path: " SYSTEM_THIS_REST
+    fi
     SYSTEM_THIS_REST="${SYSTEM_THIS_REST/#\~/$HOME}"
     if [[ ! -f "$SYSTEM_THIS_REST" ]]; then
         error "File not found: $SYSTEM_THIS_REST"
@@ -308,13 +319,15 @@ echo ""
 # =============================================================================
 sep
 ask "How do you want to pull REST submodules?"
-echo "  1) --latest   Pull the latest commit from each submodule branch"
-echo "               (may occasionally be incompatible but stays up to date)"
-echo "  2) (default)  Use the version recorded in the framework repository"
-echo "               (safer, guaranteed compatible)"
+echo "  1) --latest  (default)  Pull the latest commit from each submodule"
+echo "                          branch. Recommended for day-to-day use."
+echo "  2) Pinned                Use the versions recorded in the framework"
+echo "                          repository. Slower to update but always"
+echo "                          mutually compatible. Try this if option 1"
+echo "                          fails to build (a submodule may have drifted)."
 echo ""
-read -rp "Enter choice [1/2, default: 2]: " SUB_CHOICE
-SUB_CHOICE="${SUB_CHOICE:-2}"
+read -rp "Enter choice [1/2, default: 1]: " SUB_CHOICE
+SUB_CHOICE="${SUB_CHOICE:-1}"
 
 # =============================================================================
 #  STEP 5 -- Clone / update REST framework

From 010b10373b8a41e67b867da60bd78436f5763746 Mon Sep 17 00:00:00 2001
From: cmargalejo <cristinamargalejoblasco@gmail.com>
Date: Fri, 26 Jun 2026 11:30:27 +0200
Subject: [PATCH 4/9] Add CVMFS install mode (Mode 3) and restG4 build support

Mode 3 loads a CERN LCG view from /cvmfs (ROOT/Geant4/GSL/Garfield) and
builds only REST on top -- tested on NAF-IAXO (RHEL9, LCG_109). Includes:
- Garfield shim for the CVMFS layout (lib64, no CMake config) + Heed include flag
- temporary patches for modern Garfield (ComponentBase->Component) and the
  restG4 C++20 Geant4 check (LCG ships C++20; REST builds fine with it)
- pull the restG4 package when Geant4 is enabled
- REST_HOME set to a writable path + warning when installing under AFS $HOME
- .bashrc setup that also ensures the login profile sources it (login shells, SSH)

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 scripts/installation/install_rest.sh | 341 ++++++++++++++++++---------
 1 file changed, 223 insertions(+), 118 deletions(-)

diff --git a/scripts/installation/install_rest.sh b/scripts/installation/install_rest.sh
index 73e39e8e5..81af768bf 100644
--- a/scripts/installation/install_rest.sh
+++ b/scripts/installation/install_rest.sh
@@ -3,16 +3,18 @@
 #  REST-for-Physics -- Interactive Installation Script
 #  https://github.com/rest-for-physics/framework
 #
-#  Supports two modes:
+#  Supports three modes:
 #    1. Server install  -- ROOT/Geant4/Garfield already available (e.g. titan)
 #    2. Full install    -- Builds ROOT 6.26.10, Geant4 11.0.3, Garfield++, REST
 #                         from source (e.g. WSL / fresh Ubuntu)
+#    3. CVMFS install   -- Loads a CERN LCG view from /cvmfs for ROOT/Geant4/
+#                         Garfield and builds only REST (e.g. NAF-IAXO / RHEL9)
 #
 #  Usage:  bash install_rest.sh
 # =============================================================================
 
 # Self-fix Windows line endings before anything else
-grep -q $'\r' "$0" 2>/dev/null && sed -i 's/\r//' "$0" && exec bash "$0" "$@"
+grep -qP '\r' "$0" 2>/dev/null && sed -i 's/\r//' "$0" && exec bash "$0" "$@"
 
 set -euo pipefail
 
@@ -43,6 +45,11 @@ echo ""
 # -- GCC compatibility flags (fixes GCC 14 -Werror issues) --------------------
 GCC_COMPAT_FLAGS="-Wno-error=ignored-attributes -Wno-error=overloaded-virtual -Wno-error=maybe-uninitialized"
 
+# -- Per-mode variables (kept defined for set -u safety) ----------------------
+CMAKE_EXTRA_FLAGS=""      # extra cmake flags (e.g. Garfield Heed dir in mode 3)
+GARFIELD_HOME=""          # set by mode 3 (CVMFS shim)
+GARFIELD_SETUP=""         # set by mode 2 (path to built Garfield setupGarfield.sh)
+
 # =============================================================================
 #  STEP 0 -- Choose install mode
 # =============================================================================
@@ -52,13 +59,16 @@ echo "  1) Server install  -- use pre-installed ROOT/Geant4/Garfield on this mac
 echo "     (for clusters like titan where a system REST environment exists)"
 echo "  2) Full install    -- build ROOT, Geant4, Garfield++ and REST from source"
 echo "     (for a fresh Ubuntu / WSL system)"
+echo "  3) CVMFS install   -- load a CERN LCG view from /cvmfs for ROOT/Geant4/"
+echo "     Garfield and build only REST (for HEP clusters like NAF-IAXO / RHEL9)"
 echo ""
-read -rp "Enter choice [1/2]: " INSTALL_MODE
+read -rp "Enter choice [1/2/3]: " INSTALL_MODE
 
 case "$INSTALL_MODE" in
     1) info "Mode: Server install (using pre-built dependencies)" ;;
     2) info "Mode: Full install from source" ;;
-    *) error "Invalid choice. Please run again and enter 1 or 2." ;;
+    3) info "Mode: CVMFS install (CERN LCG view + local REST build)" ;;
+    *) error "Invalid choice. Please run again and enter 1, 2 or 3." ;;
 esac
 echo ""
 
@@ -74,6 +84,14 @@ REST_DIR="${REST_DIR/#\~/$HOME}"   # expand ~ manually
 info "REST will be installed in: $REST_DIR"
 echo ""
 
+# AFS home is small and token-based; a REST build belongs on scratch (e.g. DUST).
+if [[ "$REST_DIR" == /afs/* ]]; then
+    warn "$REST_DIR is on AFS, which is small and not suited to a REST build."
+    warn "On DESY/NAF, prefer a DUST area, e.g. /data/dust/user/<user>/rest."
+    read -rp "Use this AFS path anyway? [y/N]: " AFS_CONFIRM
+    [[ "$AFS_CONFIRM" =~ ^[Yy]$ ]] || error "Aborted. Re-run and choose a scratch/DUST path."
+fi
+
 if [[ -d "$REST_DIR" ]]; then
     warn "Directory $REST_DIR already exists."
     read -rp "Continue and use it anyway? [y/N]: " CONFIRM
@@ -87,51 +105,39 @@ if [[ "$INSTALL_MODE" == "2" ]]; then
 
     sep
     # Check for sudo access before attempting anything
-    SKIP_APT=false
     if ! sudo -v 2>/dev/null; then
-        warn "Cannot obtain sudo access."
-        warn "If system packages are already installed, you can skip this step."
-        read -rp "Skip apt package installation? [y/N]: " SKIP_APT_ANS
-        if [[ "$SKIP_APT_ANS" =~ ^[Yy]$ ]]; then
-            SKIP_APT=true
-            info "Skipping apt package installation."
-        else
-            error "Mode 2 requires sudo access to install system packages.\n       On shared servers (e.g. titan), use mode 1 instead."
-        fi
-    fi
-
-    if [[ "$SKIP_APT" == false ]]; then
-        warn "This package list was designed for Ubuntu 22/24 with ROOT 6.26.10,"
-        warn "Geant4 11.0.3 and Garfield++. It has not been fully tested on a"
-        warn "fresh system yet. If something fails, a package may be missing or"
-        warn "named differently on your Ubuntu version."
-        read -rp "Press Enter to continue or Ctrl+C to abort: "
-        echo ""
-        info "Installing system dependencies (requires sudo)..."
-        sudo apt update && sudo apt install -y \
-            build-essential cmake git wget curl \
-            gcc-11 g++-11 gfortran \
-            python3 python3-full python3-pip python3-numpy \
-            libssl-dev libxerces-c-dev libxml2-dev \
-            nlohmann-json3-dev \
-            libxxhash-dev libzstd-dev liblzma-dev liblz4-dev \
-            libfreetype6-dev \
-            libglew-dev libgl2ps-dev \
-            libx11-dev libxpm-dev libxft-dev libxext-dev \
-            libxmu-dev libxi-dev \
-            libgl1-mesa-dev libglu1-mesa-dev freeglut3-dev mesa-common-dev \
-            qtbase5-dev qtchooser qt5-qmake qtbase5-dev-tools \
-            libfftw3-dev libtinyxml2-dev libgsl-dev libglpk-dev \
-            libcfitsio-dev libcurl4-openssl-dev \
-            software-properties-common
-
-        # Python 3.10 for ROOT 6.26 compatibility
-        info "Adding deadsnakes PPA and installing Python 3.10..."
-        sudo add-apt-repository ppa:deadsnakes/ppa -y
-        sudo apt update
-        sudo apt install -y python3.10 python3.10-dev python3.10-venv
-        success "System dependencies installed."
+        error "Mode 2 requires sudo access to install system packages.\n       On shared servers (e.g. titan), use mode 1 instead."
     fi
+    warn "This package list was designed for Ubuntu 22/24 with ROOT 6.26.10,"
+    warn "Geant4 11.0.3 and Garfield++. It has not been fully tested on a"
+    warn "fresh system yet. If something fails, a package may be missing or"
+    warn "named differently on your Ubuntu version."
+    read -rp "Press Enter to continue or Ctrl+C to abort: "
+    echo ""
+    info "Installing system dependencies (requires sudo)..."
+    sudo apt update && sudo apt install -y \
+        build-essential cmake git wget curl \
+        gcc-11 g++-11 gfortran \
+        python3 python3-full python3-pip python3-numpy \
+        libssl-dev libxerces-c-dev libxml2-dev \
+        nlohmann-json3-dev \
+        libxxhash-dev libzstd-dev liblzma-dev liblz4-dev \
+        libfreetype6-dev \
+        libglew-dev libgl2ps-dev \
+        libx11-dev libxpm-dev libxft-dev libxext-dev \
+        libxmu-dev libxi-dev \
+        libgl1-mesa-dev libglu1-mesa-dev freeglut3-dev mesa-common-dev \
+        qtbase5-dev qtchooser qt5-qmake qtbase5-dev-tools \
+        libfftw3-dev libtinyxml2-dev libgsl-dev libglpk-dev \
+        libcfitsio-dev libcurl4-openssl-dev \
+        software-properties-common
+
+    # Python 3.10 for ROOT 6.26 compatibility
+    info "Adding deadsnakes PPA and installing Python 3.10..."
+    sudo add-apt-repository ppa:deadsnakes/ppa -y
+    sudo apt update
+    sudo apt install -y python3.10 python3.10-dev python3.10-venv
+    success "System dependencies installed."
     echo ""
 
     SOFTWARE_DIR="$REST_DIR/../software"
@@ -193,10 +199,8 @@ if [[ "$INSTALL_MODE" == "2" ]]; then
         -DCMAKE_CXX_COMPILER=g++-11 \
         -DGEANT4_USE_GDML=ON
     make -j"$(nproc)" install
-    # Fix ownership if files ended up root-owned (e.g. from a previous sudo run)
-    if [[ -O "$SOFTWARE_DIR/geant4-v11.0.3/install" ]]; then
-        : # Already owned by current user, nothing to do
-    else
+    # Fix ownership only if files ended up root-owned (e.g. from a previous sudo run)
+    if [[ ! -O "$SOFTWARE_DIR/geant4-v11.0.3/install" ]]; then
         sudo chown -R "$(whoami):$(whoami)" "$SOFTWARE_DIR/geant4-v11.0.3/install"
     fi
     GEANT4_SH="$SOFTWARE_DIR/geant4-v11.0.3/install/bin/geant4.sh"
@@ -231,7 +235,63 @@ if [[ "$INSTALL_MODE" == "2" ]]; then
 fi  # end MODE 2 dependencies
 
 # =============================================================================
-#  STEP 2 -- Source the environment (mode 1: system; mode 2: freshly built)
+#  MODE 3 -- CVMFS install: load a CERN LCG view + shim Garfield
+# =============================================================================
+if [[ "$INSTALL_MODE" == "3" ]]; then
+
+    sep
+    info "Mode 3 uses CERN's CVMFS software (an LCG 'view') for ROOT, Geant4,"
+    info "GSL and Garfield. Only REST itself is built locally. This survives OS"
+    info "upgrades far better than a hand-built stack."
+    echo ""
+    DEFAULT_VIEW="/cvmfs/sft.cern.ch/lcg/views/LCG_109/x86_64-el9-gcc13-opt/setup.sh"
+    ask "Path to the LCG view setup.sh:"
+    echo "  Default is tested on NAF-IAXO (RHEL9): $DEFAULT_VIEW"
+    read -rp "LCG view setup.sh [default: $DEFAULT_VIEW]: " LCG_VIEW_SETUP
+    LCG_VIEW_SETUP="${LCG_VIEW_SETUP:-$DEFAULT_VIEW}"
+    LCG_VIEW_SETUP="${LCG_VIEW_SETUP/#\~/$HOME}"
+    [[ -f "$LCG_VIEW_SETUP" ]] || error "Not found: $LCG_VIEW_SETUP\n       Check that /cvmfs is mounted and the path is correct."
+
+    info "Sourcing LCG view: $LCG_VIEW_SETUP"
+    set +u
+    source "$LCG_VIEW_SETUP"
+    set -u
+    info "ROOT $(root-config --version 2>/dev/null), Geant4 $(geant4-config --version 2>/dev/null)"
+    success "CVMFS environment loaded."
+    echo ""
+
+    # -- Garfield shim -------------------------------------------------------
+    # CVMFS Garfield ships no CMake config and uses lib64, so REST falls back to
+    # its 'old' GARFIELD_HOME detection path. We present a shim directory with
+    # the layout REST expects (lib + include), and later feed FindGarfieldOld a
+    # valid Heed include dir (it hunts for the removed HeedChamber.hh).
+    VIEW_DIR="$(dirname "$LCG_VIEW_SETUP")"
+    PLATFORM="$(basename "$VIEW_DIR")"
+    LCG_REL="$(basename "$(dirname "$VIEW_DIR")")"
+    GV="$(ls -d /cvmfs/sft.cern.ch/lcg/releases/"$LCG_REL"/Garfield++/*/"$PLATFORM" 2>/dev/null | head -1)"
+
+    if [[ -n "$GV" && -d "$GV" ]]; then
+        GLIB="lib"; [[ -d "$GV/lib64" ]] && GLIB="lib64"
+        # The shim dir lives inside REST_DIR, which must be empty for the
+        # 'git clone' in STEP 5 -- so we only compute its path here and create
+        # the actual symlinks after the clone (see STEP 5).
+        GARFIELD_HOME="$REST_DIR/garfield_home"
+        export GARFIELD_HOME
+        unset GARFIELD_INSTALL || true   # force REST's old (GARFIELD_HOME) path
+        CMAKE_EXTRA_FLAGS="-DGarfield_INCLUDE_Heed_DIRS=$GV/include/Garfield"
+        info "Garfield found: $GV ($GLIB) -- shim created after clone."
+    else
+        GARFIELD_HOME=""
+        warn "Garfield not found in $LCG_REL for platform $PLATFORM."
+        warn "If you need Garfield, choose a different LCG view; otherwise answer"
+        warn "'n' to the Garfield question below to build REST without it."
+    fi
+    echo ""
+
+fi  # end MODE 3 setup
+
+# =============================================================================
+#  STEP 2 -- Source the environment (1: system, 2: freshly built, 3: CVMFS)
 # =============================================================================
 sep
 
@@ -260,14 +320,27 @@ if [[ "$INSTALL_MODE" == "1" ]]; then
     source "$SYSTEM_THIS_REST"
     set -u
     success "System environment loaded."
+    ENV_LINES="source $SYSTEM_THIS_REST   # loads system ROOT / Geant4 / Garfield"
+elif [[ "$INSTALL_MODE" == "3" ]]; then
+    # Environment already loaded in the MODE 3 setup block above.
+    info "Using CVMFS environment from: $LCG_VIEW_SETUP"
+    if [[ -n "$GARFIELD_HOME" ]]; then
+        ENV_LINES="source $LCG_VIEW_SETUP   # CERN CVMFS LCG view (ROOT/Geant4/Garfield)
+export GARFIELD_HOME=$GARFIELD_HOME   # CVMFS Garfield shim (lib64 -> lib)"
+    else
+        ENV_LINES="source $LCG_VIEW_SETUP   # CERN CVMFS LCG view (ROOT/Geant4/Garfield)"
+    fi
 else
-    # Already sourced above during build
+    # Mode 2: ROOT/Geant4/Garfield freshly built above
     set +u
     source "$ROOT_THISROOT"
     source "$GEANT4_SH"
     source "$GARFIELD_SETUP"
     set -u
     success "Build environment loaded."
+    ENV_LINES="source $ROOT_THISROOT
+source $GEANT4_SH
+source $GARFIELD_SETUP"
 fi
 echo ""
 
@@ -319,15 +392,13 @@ echo ""
 # =============================================================================
 sep
 ask "How do you want to pull REST submodules?"
-echo "  1) --latest  (default)  Pull the latest commit from each submodule"
-echo "                          branch. Recommended for day-to-day use."
-echo "  2) Pinned                Use the versions recorded in the framework"
-echo "                          repository. Slower to update but always"
-echo "                          mutually compatible. Try this if option 1"
-echo "                          fails to build (a submodule may have drifted)."
+echo "  1) --latest   Pull the latest commit from each submodule branch"
+echo "               (may occasionally be incompatible but stays up to date)"
+echo "  2) (default)  Use the version recorded in the framework repository"
+echo "               (safer, guaranteed compatible)"
 echo ""
-read -rp "Enter choice [1/2, default: 1]: " SUB_CHOICE
-SUB_CHOICE="${SUB_CHOICE:-1}"
+read -rp "Enter choice [1/2, default: 2]: " SUB_CHOICE
+SUB_CHOICE="${SUB_CHOICE:-2}"
 
 # =============================================================================
 #  STEP 5 -- Clone / update REST framework
@@ -339,17 +410,7 @@ if [[ -d "$REST_DIR/.git" ]]; then
     git pull
 else
     info "Cloning REST framework into $REST_DIR..."
-    if [[ -d "$REST_DIR" && "$(ls -A "$REST_DIR" 2>/dev/null)" ]]; then
-        # Directory exists and is non-empty; clone to temp then move contents
-        TMPCLONE="$(mktemp -d)"
-        git clone https://github.com/rest-for-physics/framework.git "$TMPCLONE/framework"
-        shopt -s dotglob
-        mv "$TMPCLONE/framework"/* "$REST_DIR/"
-        shopt -u dotglob
-        rm -rf "$TMPCLONE"
-    else
-        git clone https://github.com/rest-for-physics/framework.git "$REST_DIR"
-    fi
+    git clone https://github.com/rest-for-physics/framework.git "$REST_DIR"
     cd "$REST_DIR"
 fi
 
@@ -360,24 +421,63 @@ fi
 info "Pulling submodules..."
 # --onlylibs skips private university repos (iaxo, detector-template, etc.)
 # that would hang waiting for SSH access most users don't have.
-# If REST_G4 is enabled, also pull the restG4 package explicitly.
 if [[ "$SUB_CHOICE" == "1" ]]; then
-    python3 "$REST_DIR/pull-submodules.py" --latest --onlylibs
+    python3 pull-submodules.py --latest --onlylibs
 else
-    # --clean asks "Are you sure?" — answer automatically to avoid consuming
-    # the main script's stdin when running non-interactively.
-    echo y | python3 "$REST_DIR/pull-submodules.py" --clean --onlylibs
+    # --clean asks "Are you sure?" -- answer automatically so it doesn't
+    # consume the script's stdin.
+    echo y | python3 pull-submodules.py --clean --onlylibs
 fi
 
 # restG4 lives in packages/, not libraries/, so --onlylibs skips it.
-# Pull it explicitly if Geant4 integration was requested.
+# Pull it explicitly if Geant4 integration / restG4 was requested.
 if [[ "$CMAKE_LIB_FLAGS" == *"REST_G4=ON"* ]]; then
     info "Pulling restG4 package..."
-    echo y | python3 "$REST_DIR/pull-submodules.py" --clean --only:restG4
+    echo y | python3 pull-submodules.py --clean --only:restG4
 fi
 success "REST framework and submodules ready."
 echo ""
 
+# -- Mode 3: create the Garfield shim now that REST_DIR exists ---------------
+# Deferred from the MODE 3 setup block: REST_DIR had to be empty for the clone.
+# Presents the CVMFS Garfield (include + lib64) in the lib/include layout REST
+# expects via GARFIELD_HOME.
+if [[ "$INSTALL_MODE" == "3" && -n "$GARFIELD_HOME" ]]; then
+    mkdir -p "$GARFIELD_HOME"
+    ln -sfn "$GV/include" "$GARFIELD_HOME/include"
+    ln -sfn "$GV/$GLIB"   "$GARFIELD_HOME/lib"
+    success "Garfield shim ready: $GARFIELD_HOME -> $GV ($GLIB)"
+fi
+
+# -- Mode 3: temporary modern-Garfield source patch --------------------------
+# CVMFS/LCG ships a modern Garfield, which renamed ComponentBase -> Component
+# (header and class). REST's detector lib still selects its USE_Garfield_OLD
+# branch here (CVMFS Garfield has no CMake config), which references the removed
+# names. Patch the old-branch names to the modern ones. This is a harmless
+# no-op once detectorlib is fixed upstream.
+# TODO: remove once detectorlib selects its modern Garfield branch on its own.
+if [[ "$INSTALL_MODE" == "3" && -n "$GARFIELD_HOME" ]]; then
+    DET_INC="$REST_DIR/source/libraries/detector/inc"
+    if [[ -f "$DET_INC/TRestDetectorGeometry.h" ]]; then
+        sed -i \
+            -e 's|#include "ComponentBase.hh"|#include "Component.hh"|' \
+            -e 's|typedef Garfield::ComponentBase Component;|typedef Garfield::Component Component;|' \
+            "$DET_INC/TRestDetectorGeometry.h" \
+            "$DET_INC/TRestDetectorGarfieldDriftProcess.h"
+        info "Applied temporary modern-Garfield (ComponentBase->Component) patch."
+    fi
+fi
+
+# -- Mode 3: let restG4 build against the CVMFS (C++20) Geant4 ----------------
+# restG4's CMake hard-requires a C++17 Geant4, but the LCG/CVMFS Geant4 11.4
+# (and ROOT 6.38) are built with C++20. REST itself builds fine with C++20, so
+# relax the check to also accept 20/23.
+# TODO: fix upstream in restG4 (accept C++17 or newer).
+if [[ "$INSTALL_MODE" == "3" && -f "$REST_DIR/source/packages/restG4/CMakeLists.txt" ]]; then
+    sed -i 's#MATCHES "17")#MATCHES "17|20|23")#' "$REST_DIR/source/packages/restG4/CMakeLists.txt"
+    info "Relaxed restG4 C++ standard check to allow C++20 (CVMFS Geant4)."
+fi
+
 # =============================================================================
 #  STEP 6 -- Configure and build
 # =============================================================================
@@ -417,7 +517,7 @@ cmake "$REST_DIR" \
     -DCMAKE_INSTALL_PREFIX="$INSTALL_DIR" \
     -DCMAKE_BUILD_TYPE=Release \
     -DCMAKE_CXX_FLAGS="$GCC_COMPAT_FLAGS" \
-    $CMAKE_LIB_FLAGS
+    $CMAKE_LIB_FLAGS $CMAKE_EXTRA_FLAGS
 
 echo ""
 info "Building REST with $NJOBS parallel jobs..."
@@ -447,7 +547,6 @@ echo ""
 #  STEP 8 -- Optional: add to .bashrc
 # =============================================================================
 sep
-# Flush any leftover input from the build output before asking
 # Flush leftover keystrokes only when running interactively
 [[ -t 0 ]] && { read -r -t 0.1 -n 10000 discard 2>/dev/null || true; }
 ask "How do you want to set up your ~/.bashrc?"
@@ -462,52 +561,54 @@ BASHRC_CHOICE="${BASHRC_CHOICE:-1}"
 
 case "$BASHRC_CHOICE" in
     1|2)
+        # ENV_LINES (set in STEP 2) loads the dependency environment for the
+        # chosen mode. Full setup also sources the local REST; system-only
+        # leaves it commented for the user to enable manually.
         if [[ "$BASHRC_CHOICE" == "1" ]]; then
-            # Full setup: system env + local REST
-            if [[ "$INSTALL_MODE" == "1" ]]; then
-                BASHRC_BLOCK="
-# -- REST-for-Physics ---------------------------------------------------------
-source \"$SYSTEM_THIS_REST\"   # loads system ROOT / Geant4 / Garfield
-source \"$INSTALL_DIR/thisREST.sh\"   # your local REST install
-# -----------------------------------------------------------------------------"
-            else
-                BASHRC_BLOCK="
-# -- REST-for-Physics ---------------------------------------------------------
-source \"$ROOT_THISROOT\"
-source \"$GEANT4_SH\"
-source \"$GARFIELD_SETUP\"
-source \"$INSTALL_DIR/thisREST.sh\"   # your local REST install
-# -----------------------------------------------------------------------------"
+            LOCAL_LINE="source $INSTALL_DIR/thisREST.sh   # your local REST install"
+            # On NAF $HOME is AFS (not writable in-session); REST stores its
+            # .rest dir under $REST_HOME, which thisREST.sh sets to $HOME -- so
+            # override it AFTER sourcing, to a writable path.
+            if [[ "$INSTALL_MODE" == "3" ]]; then
+                LOCAL_LINE="$LOCAL_LINE
+export REST_HOME=$REST_DIR   # REST .rest dir on writable disk (AFS \$HOME is not writable)"
             fi
             CHECK_LINE="$INSTALL_DIR/thisREST.sh"
         else
-            # System only
-            if [[ "$INSTALL_MODE" == "1" ]]; then
-                BASHRC_BLOCK="
-# -- REST-for-Physics ---------------------------------------------------------
-source \"$SYSTEM_THIS_REST\"   # loads system ROOT / Geant4 / Garfield
-# source \"$INSTALL_DIR/thisREST.sh\"   # uncomment to use your local REST build
-# -----------------------------------------------------------------------------"
-            else
-                BASHRC_BLOCK="
-# -- REST-for-Physics ---------------------------------------------------------
-source \"$ROOT_THISROOT\"
-source \"$GEANT4_SH\"
-source \"$GARFIELD_SETUP\"
-# source \"$INSTALL_DIR/thisREST.sh\"   # uncomment to use your local REST build
-# -----------------------------------------------------------------------------"
-            fi
+            LOCAL_LINE="# source $INSTALL_DIR/thisREST.sh   # uncomment to use your local REST build"
             CHECK_LINE="REST-for-Physics"
             info "Your local REST is installed at: $INSTALL_DIR/thisREST.sh"
             info "Source it manually any time you want to switch to your local build."
         fi
 
-        # Avoid duplicate entries
-        if grep -qF "$CHECK_LINE" ~/.bashrc 2>/dev/null; then
-            warn "~/.bashrc already contains a REST entry -- skipping."
+        BASHRC_BLOCK="
+# -- REST-for-Physics ---------------------------------------------------------
+$ENV_LINES
+$LOCAL_LINE
+# -----------------------------------------------------------------------------"
+
+        # The REST block goes in ~/.bashrc (canonical for interactive shells).
+        RC_FILE="$HOME/.bashrc"
+        if grep -qF "$CHECK_LINE" "$RC_FILE" 2>/dev/null; then
+            warn "$RC_FILE already contains a REST entry -- skipping."
+        else
+            echo "$BASHRC_BLOCK" >> "$RC_FILE"
+            success "Added REST setup to $RC_FILE."
+        fi
+
+        # Login shells (e.g. SSH on NAF) read a profile file, NOT ~/.bashrc, so
+        # make sure the login profile sources ~/.bashrc -- otherwise REST would
+        # not load on login. (Ubuntu's default ~/.profile already does this.)
+        LOGIN_FILE=""
+        for f in "$HOME/.bash_profile" "$HOME/.bash_login" "$HOME/.profile"; do
+            [[ -f "$f" ]] && { LOGIN_FILE="$f"; break; }
+        done
+        [[ -z "$LOGIN_FILE" ]] && LOGIN_FILE="$HOME/.bash_profile"  # none exists: create standard one
+        if grep -q '\.bashrc' "$LOGIN_FILE" 2>/dev/null; then
+            info "$LOGIN_FILE already sources ~/.bashrc."
         else
-            echo "$BASHRC_BLOCK" >> ~/.bashrc
-            success "Added to ~/.bashrc."
+            printf '\n# Source ~/.bashrc for login shells (added by REST installer)\n[ -f ~/.bashrc ] && . ~/.bashrc\n' >> "$LOGIN_FILE"
+            success "Updated $LOGIN_FILE to source ~/.bashrc (needed for login shells, e.g. SSH)."
         fi
 
         # ROOT browser fix
@@ -541,8 +642,12 @@ echo -e "${RESET}"
 echo "  To activate REST (if not already in your ~/.bashrc):"
 if [[ "$INSTALL_MODE" == "1" ]]; then
     echo "    source $SYSTEM_THIS_REST   # system ROOT/Geant4/Garfield"
+elif [[ "$INSTALL_MODE" == "3" ]]; then
+    echo "    source $LCG_VIEW_SETUP   # CVMFS ROOT/Geant4/Garfield"
+    [[ -n "$GARFIELD_HOME" ]] && echo "    export GARFIELD_HOME=$GARFIELD_HOME"
 fi
 echo "    source $INSTALL_DIR/thisREST.sh   # your local REST build"
+[[ "$INSTALL_MODE" == "3" ]] && echo "    export REST_HOME=$REST_DIR   # REST .rest dir (AFS \$HOME is not writable)"
 echo ""
 echo "  Quick test:    restRoot"
 echo "  Docs:          https://rest-for-physics.github.io"
@@ -561,4 +666,4 @@ echo "  |          Welcome to REST-for-Physics!                |"
 echo "  |                                                      |"
 echo "  +------------------------------------------------------+"
 echo -e "${RESET}"
-echo ""
+echo ""
\ No newline at end of file

From 882a166c7e6fd9570a0b793f7ed9b95fc9a795d6 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 26 Jun 2026 09:31:35 +0000
Subject: [PATCH 5/9] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 scripts/installation/install_rest.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/installation/install_rest.sh b/scripts/installation/install_rest.sh
index 81af768bf..54674d8f1 100644
--- a/scripts/installation/install_rest.sh
+++ b/scripts/installation/install_rest.sh
@@ -666,4 +666,4 @@ echo "  |          Welcome to REST-for-Physics!                |"
 echo "  |                                                      |"
 echo "  +------------------------------------------------------+"
 echo -e "${RESET}"
-echo ""
\ No newline at end of file
+echo ""

From a44d5b1ef8ca6b0c58c334d1cdef11c4e0fddb1c Mon Sep 17 00:00:00 2001
From: cmargalejo <cristinamargalejoblasco@gmail.com>
Date: Fri, 26 Jun 2026 11:45:04 +0200
Subject: [PATCH 6/9] Silence Garfield cling autoload warnings in CVMFS mode

Garfield's ROOT dictionary records its headers under "Include/Garfield/" (capital
I, old layout), but LCG installs them lowercase, so cling prints ~50 harmless
"Missing FileEntry" warnings at restRoot startup. Add a capital-Include symlink
to the Garfield shim and put it on ROOT_INCLUDE_PATH (in the Mode 3 .bashrc),
which makes the warnings go away. Verified on NAF-IAXO.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 scripts/installation/install_rest.sh | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/scripts/installation/install_rest.sh b/scripts/installation/install_rest.sh
index 54674d8f1..bd6f028c0 100644
--- a/scripts/installation/install_rest.sh
+++ b/scripts/installation/install_rest.sh
@@ -446,6 +446,11 @@ if [[ "$INSTALL_MODE" == "3" && -n "$GARFIELD_HOME" ]]; then
     mkdir -p "$GARFIELD_HOME"
     ln -sfn "$GV/include" "$GARFIELD_HOME/include"
     ln -sfn "$GV/$GLIB"   "$GARFIELD_HOME/lib"
+    # Capital-I 'Include' (-> the lowercase include): lets cling resolve the
+    # Garfield dictionary's autoload header paths (Include/Garfield/*.hh) and so
+    # silences ~50 harmless "Missing FileEntry" warnings at restRoot startup.
+    # (Used together with ROOT_INCLUDE_PATH below.)
+    ln -sfn include "$GARFIELD_HOME/Include"
     success "Garfield shim ready: $GARFIELD_HOME -> $GV ($GLIB)"
 fi
 
@@ -572,6 +577,10 @@ case "$BASHRC_CHOICE" in
             if [[ "$INSTALL_MODE" == "3" ]]; then
                 LOCAL_LINE="$LOCAL_LINE
 export REST_HOME=$REST_DIR   # REST .rest dir on writable disk (AFS \$HOME is not writable)"
+                if [[ -n "$GARFIELD_HOME" ]]; then
+                    LOCAL_LINE="$LOCAL_LINE
+export ROOT_INCLUDE_PATH=$GARFIELD_HOME:\$ROOT_INCLUDE_PATH   # silence Garfield cling autoload warnings"
+                fi
             fi
             CHECK_LINE="$INSTALL_DIR/thisREST.sh"
         else
@@ -666,4 +675,4 @@ echo "  |          Welcome to REST-for-Physics!                |"
 echo "  |                                                      |"
 echo "  +------------------------------------------------------+"
 echo -e "${RESET}"
-echo ""
+echo ""
\ No newline at end of file

From 14c8535c2a48732ef06b70e246ed92162cfec9c6 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 26 Jun 2026 09:45:22 +0000
Subject: [PATCH 7/9] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 scripts/installation/install_rest.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/installation/install_rest.sh b/scripts/installation/install_rest.sh
index bd6f028c0..6f299c527 100644
--- a/scripts/installation/install_rest.sh
+++ b/scripts/installation/install_rest.sh
@@ -675,4 +675,4 @@ echo "  |          Welcome to REST-for-Physics!                |"
 echo "  |                                                      |"
 echo "  +------------------------------------------------------+"
 echo -e "${RESET}"
-echo ""
\ No newline at end of file
+echo ""

From 43e2bd6aa11b17eeda6d3bd4784bab7abed1b155 Mon Sep 17 00:00:00 2001
From: cmargalejo <cristinamargalejoblasco@gmail.com>
Date: Mon, 29 Jun 2026 10:33:42 +0200
Subject: [PATCH 8/9] Default submodules to --latest; document Mode 3 (CVMFS)
 in README

- Restore --latest as the default submodule strategy (option 2 = pinned remains
  available, recommended if a latest build fails). Reverts the pinned default
  introduced during the Mode 3 merge, back to the PR's original intent.
- README: add the Mode 3 (CVMFS) section, note restG4 is pulled when Geant4 is
  enabled, the login-shell .bashrc sourcing, and CVMFS/RHEL9 under requirements.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 scripts/installation/README.md       | 28 ++++++++++++++++++++++++----
 scripts/installation/install_rest.sh | 14 ++++++++------
 2 files changed, 32 insertions(+), 10 deletions(-)

diff --git a/scripts/installation/README.md b/scripts/installation/README.md
index 310ca1633..64136d002 100644
--- a/scripts/installation/README.md
+++ b/scripts/installation/README.md
@@ -37,22 +37,41 @@ System dependencies are installed via `apt` (requires `sudo`).
 If `sudo` is not available the script offers to skip this step, assuming
 packages are already present.
 
+### Mode 3 -- CVMFS install
+
+For HEP clusters where CERN's CVMFS is mounted (e.g. NAF-IAXO at DESY, RHEL 9).
+Instead of building the dependencies, the script loads a CERN **LCG view** from
+`/cvmfs` (providing ROOT, Geant4, GSL and Garfield) and builds only REST on top.
+This needs no `sudo` and survives OS upgrades far better than a hand-built stack.
+
+You will be asked for the LCG view `setup.sh` (default: a tested el9 view,
+`LCG_109/x86_64-el9-gcc13-opt`). The script then sets up a small Garfield
+compatibility shim, clones REST, and builds it -- including `restG4` if Geant4
+integration is enabled.
+
+On clusters where `$HOME` is on AFS (not writable in-session), the script sets
+`REST_HOME` to a writable location so REST's per-user `.rest` directory works.
+
 ## What the script does
 
 1. Installs system packages (mode 2, optional)
-2. Downloads and builds ROOT, Geant4, Garfield++ (mode 2)
+2. Downloads and builds ROOT, Geant4, Garfield++ (mode 2),
+   or loads a CERN LCG view from `/cvmfs` (mode 3)
 3. Asks you to choose which REST libraries to enable
 4. Clones the REST framework and pulls submodules
+   (also the `restG4` package when Geant4 integration is enabled)
 5. Configures and builds REST with CMake
 6. Tests the installation (`restRoot`)
 7. Optionally adds the environment setup to `~/.bashrc`
+   (and ensures login shells source it, e.g. for SSH)
 
 ## Options asked during installation
 
 - **Install directory** -- where REST source and build will live (default: `~/rest`)
 - **Libraries** -- all, a common subset, or pick individually
 - **Garfield++ / Geant4 integration** -- enable or disable
-- **Submodule strategy** -- latest commits or framework-pinned versions
+- **Submodule strategy** -- latest commits (default) or framework-pinned versions
+  (pick pinned if a latest build fails to compile)
 - **Parallel jobs** -- capped at 16 for shared-server politeness
 
 ## Individual scripts (legacy)
@@ -68,7 +87,8 @@ The older per-package scripts are still available for reference:
 
 ## Requirements
 
-- **OS**: Ubuntu 22.04 / 24.04 (or WSL with either). Other Linux distros may
-  work but the `apt` package list would need adapting.
+- **OS**: Ubuntu 22.04 / 24.04 (or WSL with either) for mode 2; any Linux with
+  CERN CVMFS mounted for mode 3 (e.g. RHEL 9 / NAF). Other distros may work but
+  the mode-2 `apt` package list would need adapting.
 - **Disk**: ~5 GB for a full build (ROOT + Geant4 + Garfield + REST)
 - **Tools**: `bash`, `git`, `python3`, `cmake`, `make`, `wget`
diff --git a/scripts/installation/install_rest.sh b/scripts/installation/install_rest.sh
index 6f299c527..02e4a19d0 100644
--- a/scripts/installation/install_rest.sh
+++ b/scripts/installation/install_rest.sh
@@ -392,13 +392,15 @@ echo ""
 # =============================================================================
 sep
 ask "How do you want to pull REST submodules?"
-echo "  1) --latest   Pull the latest commit from each submodule branch"
-echo "               (may occasionally be incompatible but stays up to date)"
-echo "  2) (default)  Use the version recorded in the framework repository"
-echo "               (safer, guaranteed compatible)"
+echo "  1) (default)  --latest -- pull the latest commit from each submodule"
+echo "                branch (newest features; may occasionally be momentarily"
+echo "                incompatible across submodules)"
+echo "  2) Pinned     use the versions recorded in the framework repository"
+echo "                (reproducible / guaranteed compatible -- try this if"
+echo "                option 1 fails to build)"
 echo ""
-read -rp "Enter choice [1/2, default: 2]: " SUB_CHOICE
-SUB_CHOICE="${SUB_CHOICE:-2}"
+read -rp "Enter choice [1/2, default: 1]: " SUB_CHOICE
+SUB_CHOICE="${SUB_CHOICE:-1}"
 
 # =============================================================================
 #  STEP 5 -- Clone / update REST framework

From 334812c04b50dbf9e2469c714aef2d913d0d6816 Mon Sep 17 00:00:00 2001
From: cmargalejo <cristinamargalejoblasco@gmail.com>
Date: Mon, 29 Jun 2026 10:35:27 +0200
Subject: [PATCH 9/9] Reword submodule option 2 as --clean (matches the
 flag/terminology)

Use "--clean" instead of "Pinned" for the framework-recorded submodule versions,
consistent with the pull-submodules.py --clean flag and the project's wording.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 scripts/installation/README.md       | 4 ++--
 scripts/installation/install_rest.sh | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/installation/README.md b/scripts/installation/README.md
index 64136d002..af4b6cacf 100644
--- a/scripts/installation/README.md
+++ b/scripts/installation/README.md
@@ -70,8 +70,8 @@ On clusters where `$HOME` is on AFS (not writable in-session), the script sets
 - **Install directory** -- where REST source and build will live (default: `~/rest`)
 - **Libraries** -- all, a common subset, or pick individually
 - **Garfield++ / Geant4 integration** -- enable or disable
-- **Submodule strategy** -- latest commits (default) or framework-pinned versions
-  (pick pinned if a latest build fails to compile)
+- **Submodule strategy** -- `--latest` commits (default) or the `--clean`
+  framework-recorded versions (pick `--clean` if a latest build fails to compile)
 - **Parallel jobs** -- capped at 16 for shared-server politeness
 
 ## Individual scripts (legacy)
diff --git a/scripts/installation/install_rest.sh b/scripts/installation/install_rest.sh
index 02e4a19d0..9116e258b 100644
--- a/scripts/installation/install_rest.sh
+++ b/scripts/installation/install_rest.sh
@@ -395,7 +395,7 @@ ask "How do you want to pull REST submodules?"
 echo "  1) (default)  --latest -- pull the latest commit from each submodule"
 echo "                branch (newest features; may occasionally be momentarily"
 echo "                incompatible across submodules)"
-echo "  2) Pinned     use the versions recorded in the framework repository"
+echo "  2) --clean    use the versions recorded in the framework repository"
 echo "                (reproducible / guaranteed compatible -- try this if"
 echo "                option 1 fails to build)"
 echo ""