From bef23f7e59338ebd2ed7415b8221e1416bba5075 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 20:45:15 +0200
Subject: [PATCH 01/69] compilation binary

---
 .github/workflows/compile_madng.yml | 50 +++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100644 .github/workflows/compile_madng.yml

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
new file mode 100644
index 0000000..8ad5d99
--- /dev/null
+++ b/.github/workflows/compile_madng.yml
@@ -0,0 +1,50 @@
+# This workflow will install Python dependencies, run tests on a variety Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Make a MAD-NG Binary
+
+on:
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+
+    steps:
+    - name: Checkout current repo
+      uses: actions/checkout@v6
+
+    - name: Clone another repo
+      uses: actions/checkout@v6
+      with:
+        repository: MethodicalAcceleratorDesign/MAD-NG
+        path: MAD
+
+    - name: Select Makefile
+      run: |
+        if [ "$RUNNER_OS" = "Linux" ]; then
+          cp MAD/src/makefile.lxplus MAD/src/Makefile
+        elif [ "$RUNNER_OS" = "macOS" ]; then
+          cp MAD/src/makefile.macos MAD/src/Makefile
+        else
+          echo "Unsupported OS: $RUNNER_OS"
+          exit 1
+        fi
+
+    - name: Compile MAD-NG
+      run: |
+        cd MAD/src
+        make -j
+
+    - name: Upload it
+    - uses: actions/upload-artifact@v7
+      with:
+        name: executable-${{ runner.os }}
+        path: MAD/src/mad
\ No newline at end of file

From 860070b11590986687f8c44b51d52fb8f82f8e70 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 20:47:57 +0200
Subject: [PATCH 02/69] compilation binary

---
 .github/workflows/compile_madng.yml | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 8ad5d99..3ccd2d0 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -39,12 +39,11 @@ jobs:
         fi
 
     - name: Compile MAD-NG
-      run: |
-        cd MAD/src
-        make -j
+      working-directory: MAD/src
+      run: make -j
 
     - name: Upload it
-    - uses: actions/upload-artifact@v7
+      uses: actions/upload-artifact@v7
       with:
         name: executable-${{ runner.os }}
-        path: MAD/src/mad
\ No newline at end of file
+        path: MAD/src/mad

From 9e02a45bfb6c8a1ecd35b4cc6cd7bf1e387cb5ed Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 21:28:16 +0200
Subject: [PATCH 03/69] Add staging scripts for MAD-NG headers on Linux and
 macOS

---
 .github/workflows/compile_madng.yml |  16 +++
 tools/stage_madng_headers_linux.sh  | 165 ++++++++++++++++++++++++++++
 tools/stage_madng_headers_macos.sh  | 165 ++++++++++++++++++++++++++++
 3 files changed, 346 insertions(+)
 create mode 100755 tools/stage_madng_headers_linux.sh
 create mode 100755 tools/stage_madng_headers_macos.sh

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 8f16d73..297c1a0 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -39,6 +39,22 @@ jobs:
           exit 1
         fi
 
+    - name: Stage MAD-NG headers
+      run: |
+        mkdir -p MAD/tools
+        cp -f tools/stage_madng_headers_linux.sh MAD/tools/ || true
+        cp -f tools/stage_madng_headers_macos.sh MAD/tools/ || true
+        chmod +x MAD/tools/stage_madng_headers_*.sh
+
+        if [ "$RUNNER_OS" = "Linux" ]; then
+          (cd MAD && ./tools/stage_madng_headers_linux.sh)
+        elif [ "$RUNNER_OS" = "macOS" ]; then
+          (cd MAD && ./tools/stage_madng_headers_macos.sh)
+        else
+          echo "Unsupported OS: $RUNNER_OS"
+          exit 1
+        fi
+
     - name: Install Linux dependencies
       if: runner.os == 'Linux'
       run: |
diff --git a/tools/stage_madng_headers_linux.sh b/tools/stage_madng_headers_linux.sh
new file mode 100755
index 0000000..c74534a
--- /dev/null
+++ b/tools/stage_madng_headers_linux.sh
@@ -0,0 +1,165 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Stage headers into the layout expected by MAD-NG's unmodified `src/Makefile`.
+#
+# Expected include paths (from `src/Makefile`):
+#   -I../lib/luajit/src            -> lua.h, luaconf.h, lualib.h, lauxlib.h, lua.hpp
+#   -I../lib/nlopt/src/api         -> nlopt.h
+#   -I../lib/fftw3/api             -> fftw3.h
+#   -I../lib/nfft3/include         -> nfft3.h (and friends)
+#
+# This script does NOT build archives; it only ensures headers exist (by
+# downloading sources, or by symlinking/copying from user-provided locations).
+
+ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+LIB_DIR="${ROOT}/lib"
+
+LUAJIT_REF="${LUAJIT_REF:-mad-patch}"
+LUAJIT_REPO="${LUAJIT_REPO:-https://github.com/MethodicalAcceleratorDesign/LuaJIT.git}"
+
+NLOPT_REF="${NLOPT_REF:-v2.7.1}"
+NLOPT_REPO="${NLOPT_REPO:-https://github.com/stevengj/nlopt.git}"
+
+FFTW_VERSION="${FFTW_VERSION:-3.3.10}"
+NFFT_VERSION="${NFFT_VERSION:-3.5.3}"
+
+# Optional: point these at already-installed headers (will be copied/symlinked)
+LUAJIT_SRC_DIR="${LUAJIT_SRC_DIR:-}"   # directory containing lua.h etc
+NLOPT_INC_DIR="${NLOPT_INC_DIR:-}"     # directory containing nlopt.h
+FFTW_INC_DIR="${FFTW_INC_DIR:-}"       # directory containing fftw3.h
+NFFT_INC_DIR="${NFFT_INC_DIR:-}"       # directory containing nfft3.h
+
+need_cmd() {
+  command -v "$1" >/dev/null 2>&1 || { echo "Missing command: $1" >&2; exit 1; }
+}
+
+fetch_tarball() {
+  local url="$1"
+  local out="$2"
+  if [[ -f "${out}" ]]; then return 0; fi
+  if command -v curl >/dev/null 2>&1; then
+    curl -L --fail "${url}" -o "${out}"
+  else
+    need_cmd wget
+    wget -O "${out}" "${url}"
+  fi
+}
+
+stage_dir_copy_or_link() {
+  local src="$1"
+  local dest="$2"
+  local mode="${3:-symlink}" # symlink|copy
+  rm -rf "${dest}"
+  mkdir -p "$(dirname "${dest}")"
+  case "${mode}" in
+    symlink) ln -s "${src}" "${dest}" ;;
+    copy) cp -a "${src}" "${dest}" ;;
+    *) echo "Unknown mode: ${mode}" >&2; exit 1 ;;
+  esac
+}
+
+stage_file_copy_or_link() {
+  local src="$1"
+  local dest="$2"
+  local mode="${3:-symlink}" # symlink|copy
+  rm -f "${dest}"
+  mkdir -p "$(dirname "${dest}")"
+  case "${mode}" in
+    symlink) ln -s "${src}" "${dest}" ;;
+    copy) cp -a "${src}" "${dest}" ;;
+    *) echo "Unknown mode: ${mode}" >&2; exit 1 ;;
+  esac
+}
+
+main() {
+  mkdir -p "${LIB_DIR}"
+
+  # LuaJIT headers -> lib/luajit/src/*
+  if [[ -n "${LUAJIT_SRC_DIR}" ]]; then
+    echo "Staging LuaJIT headers from LUAJIT_SRC_DIR=${LUAJIT_SRC_DIR}"
+    mkdir -p "${LIB_DIR}/luajit"
+    stage_dir_copy_or_link "${LUAJIT_SRC_DIR}" "${LIB_DIR}/luajit/src" "symlink"
+  else
+    echo "Fetching LuaJIT repo for headers (${LUAJIT_REF})"
+    need_cmd git
+    local_dir="${LIB_DIR}/luajit"
+    if [[ ! -d "${local_dir}/.git" ]]; then
+      git clone "${LUAJIT_REPO}" "${local_dir}"
+    fi
+    ( cd "${local_dir}"
+      git fetch --all --tags
+      git checkout "${LUAJIT_REF}"
+      git pull --ff-only || true
+    )
+  fi
+
+  # NLOpt headers -> lib/nlopt/src/api/nlopt.h
+  if [[ -n "${NLOPT_INC_DIR}" ]]; then
+    echo "Staging NLOpt header from NLOPT_INC_DIR=${NLOPT_INC_DIR}"
+    stage_file_copy_or_link "${NLOPT_INC_DIR}/nlopt.h" "${LIB_DIR}/nlopt/src/api/nlopt.h" "symlink"
+  else
+    echo "Fetching NLOpt repo for headers (${NLOPT_REF})"
+    need_cmd git
+    local_dir="${LIB_DIR}/nlopt"
+    if [[ ! -d "${local_dir}/.git" ]]; then
+      git clone "${NLOPT_REPO}" "${local_dir}"
+    fi
+    ( cd "${local_dir}"
+      git fetch --all --tags
+      git checkout "${NLOPT_REF}"
+      git pull --ff-only || true
+    )
+  fi
+
+  # FFTW headers -> lib/fftw3/api/fftw3.h
+  if [[ -n "${FFTW_INC_DIR}" ]]; then
+    echo "Staging FFTW header from FFTW_INC_DIR=${FFTW_INC_DIR}"
+    stage_file_copy_or_link "${FFTW_INC_DIR}/fftw3.h" "${LIB_DIR}/fftw3/api/fftw3.h" "symlink"
+  else
+    echo "Fetching FFTW tarball for headers (${FFTW_VERSION})"
+    need_cmd tar
+    tar_name="fftw-${FFTW_VERSION}.tar.gz"
+    tar_path="${LIB_DIR}/${tar_name}"
+    url="https://fftw.org/${tar_name}"
+    fetch_tarball "${url}" "${tar_path}"
+    ( cd "${LIB_DIR}" && tar xzf "${tar_name}" )
+    rm -f "${LIB_DIR}/fftw3"
+    ln -s "fftw-${FFTW_VERSION}" "${LIB_DIR}/fftw3"
+  fi
+
+  # NFFT headers -> lib/nfft3/include/nfft3.h
+  if [[ -n "${NFFT_INC_DIR}" ]]; then
+    echo "Staging NFFT header from NFFT_INC_DIR=${NFFT_INC_DIR}"
+    mkdir -p "${LIB_DIR}/nfft3"
+    stage_dir_copy_or_link "${NFFT_INC_DIR}" "${LIB_DIR}/nfft3/include" "symlink"
+  else
+    echo "Fetching NFFT tarball for headers (${NFFT_VERSION})"
+    need_cmd tar
+    tar_name="nfft-${NFFT_VERSION}.tar.gz"
+    tar_path="${LIB_DIR}/${tar_name}"
+    url="http://www.nfft.org/download/${tar_name}"
+    fetch_tarball "${url}" "${tar_path}"
+    ( cd "${LIB_DIR}" && tar xzf "${tar_name}" )
+    rm -f "${LIB_DIR}/nfft3"
+    ln -s "nfft-${NFFT_VERSION}" "${LIB_DIR}/nfft3"
+  fi
+
+  echo
+  echo "Header checks (expected by src/Makefile):"
+  for f in \
+    "${LIB_DIR}/luajit/src/lua.h" \
+    "${LIB_DIR}/nlopt/src/api/nlopt.h" \
+    "${LIB_DIR}/fftw3/api/fftw3.h" \
+    "${LIB_DIR}/nfft3/include/nfft3.h"
+  do
+    if [[ -e "${f}" ]]; then
+      echo "  OK  ${f}"
+    else
+      echo "  MISS ${f}"
+    fi
+  done
+}
+
+main "$@"
+
diff --git a/tools/stage_madng_headers_macos.sh b/tools/stage_madng_headers_macos.sh
new file mode 100755
index 0000000..44f5b59
--- /dev/null
+++ b/tools/stage_madng_headers_macos.sh
@@ -0,0 +1,165 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Stage headers into the layout expected by MAD-NG's unmodified `src/Makefile`.
+#
+# Expected include paths (from `src/Makefile`):
+#   -I../lib/luajit/src            -> lua.h etc
+#   -I../lib/nlopt/src/api         -> nlopt.h
+#   -I../lib/fftw3/api             -> fftw3.h
+#   -I../lib/nfft3/include         -> nfft3.h
+#
+# This script does NOT build archives; it only ensures headers exist (by
+# downloading sources, or by symlinking/copying from user-provided locations).
+
+ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+LIB_DIR="${ROOT}/lib"
+
+LUAJIT_REF="${LUAJIT_REF:-mad-patch}"
+LUAJIT_REPO="${LUAJIT_REPO:-https://github.com/MethodicalAcceleratorDesign/LuaJIT.git}"
+
+NLOPT_REF="${NLOPT_REF:-v2.7.1}"
+NLOPT_REPO="${NLOPT_REPO:-https://github.com/stevengj/nlopt.git}"
+
+FFTW_VERSION="${FFTW_VERSION:-3.3.10}"
+NFFT_VERSION="${NFFT_VERSION:-3.5.3}"
+
+# Optional: point these at already-installed headers (will be copied/symlinked)
+LUAJIT_SRC_DIR="${LUAJIT_SRC_DIR:-}"   # directory containing lua.h etc
+NLOPT_INC_DIR="${NLOPT_INC_DIR:-}"     # directory containing nlopt.h
+FFTW_INC_DIR="${FFTW_INC_DIR:-}"       # directory containing fftw3.h
+NFFT_INC_DIR="${NFFT_INC_DIR:-}"       # directory containing nfft3.h
+
+need_cmd() {
+  command -v "$1" >/dev/null 2>&1 || { echo "Missing command: $1" >&2; exit 1; }
+}
+
+fetch_tarball() {
+  local url="$1"
+  local out="$2"
+  if [[ -f "${out}" ]]; then return 0; fi
+  if command -v curl >/dev/null 2>&1; then
+    curl -L --fail "${url}" -o "${out}"
+  else
+    need_cmd wget
+    wget -O "${out}" "${url}"
+  fi
+}
+
+stage_dir_copy_or_link() {
+  local src="$1"
+  local dest="$2"
+  local mode="${3:-symlink}" # symlink|copy
+  rm -rf "${dest}"
+  mkdir -p "$(dirname "${dest}")"
+  case "${mode}" in
+    symlink) ln -s "${src}" "${dest}" ;;
+    copy) cp -a "${src}" "${dest}" ;;
+    *) echo "Unknown mode: ${mode}" >&2; exit 1 ;;
+  esac
+}
+
+stage_file_copy_or_link() {
+  local src="$1"
+  local dest="$2"
+  local mode="${3:-symlink}" # symlink|copy
+  rm -f "${dest}"
+  mkdir -p "$(dirname "${dest}")"
+  case "${mode}" in
+    symlink) ln -s "${src}" "${dest}" ;;
+    copy) cp -a "${src}" "${dest}" ;;
+    *) echo "Unknown mode: ${mode}" >&2; exit 1 ;;
+  esac
+}
+
+main() {
+  mkdir -p "${LIB_DIR}"
+
+  # LuaJIT headers -> lib/luajit/src/*
+  if [[ -n "${LUAJIT_SRC_DIR}" ]]; then
+    echo "Staging LuaJIT headers from LUAJIT_SRC_DIR=${LUAJIT_SRC_DIR}"
+    mkdir -p "${LIB_DIR}/luajit"
+    stage_dir_copy_or_link "${LUAJIT_SRC_DIR}" "${LIB_DIR}/luajit/src" "symlink"
+  else
+    echo "Fetching LuaJIT repo for headers (${LUAJIT_REF})"
+    need_cmd git
+    local_dir="${LIB_DIR}/luajit"
+    if [[ ! -d "${local_dir}/.git" ]]; then
+      git clone "${LUAJIT_REPO}" "${local_dir}"
+    fi
+    ( cd "${local_dir}"
+      git fetch --all --tags
+      git checkout "${LUAJIT_REF}"
+      git pull --ff-only || true
+    )
+  fi
+
+  # NLOpt headers -> lib/nlopt/src/api/nlopt.h
+  if [[ -n "${NLOPT_INC_DIR}" ]]; then
+    echo "Staging NLOpt header from NLOPT_INC_DIR=${NLOPT_INC_DIR}"
+    stage_file_copy_or_link "${NLOPT_INC_DIR}/nlopt.h" "${LIB_DIR}/nlopt/src/api/nlopt.h" "symlink"
+  else
+    echo "Fetching NLOpt repo for headers (${NLOPT_REF})"
+    need_cmd git
+    local_dir="${LIB_DIR}/nlopt"
+    if [[ ! -d "${local_dir}/.git" ]]; then
+      git clone "${NLOPT_REPO}" "${local_dir}"
+    fi
+    ( cd "${local_dir}"
+      git fetch --all --tags
+      git checkout "${NLOPT_REF}"
+      git pull --ff-only || true
+    )
+  fi
+
+  # FFTW headers -> lib/fftw3/api/fftw3.h
+  if [[ -n "${FFTW_INC_DIR}" ]]; then
+    echo "Staging FFTW header from FFTW_INC_DIR=${FFTW_INC_DIR}"
+    stage_file_copy_or_link "${FFTW_INC_DIR}/fftw3.h" "${LIB_DIR}/fftw3/api/fftw3.h" "symlink"
+  else
+    echo "Fetching FFTW tarball for headers (${FFTW_VERSION})"
+    need_cmd tar
+    tar_name="fftw-${FFTW_VERSION}.tar.gz"
+    tar_path="${LIB_DIR}/${tar_name}"
+    url="https://fftw.org/${tar_name}"
+    fetch_tarball "${url}" "${tar_path}"
+    ( cd "${LIB_DIR}" && tar xzf "${tar_name}" )
+    rm -f "${LIB_DIR}/fftw3"
+    ln -s "fftw-${FFTW_VERSION}" "${LIB_DIR}/fftw3"
+  fi
+
+  # NFFT headers -> lib/nfft3/include/nfft3.h
+  if [[ -n "${NFFT_INC_DIR}" ]]; then
+    echo "Staging NFFT header(s) from NFFT_INC_DIR=${NFFT_INC_DIR}"
+    mkdir -p "${LIB_DIR}/nfft3"
+    stage_dir_copy_or_link "${NFFT_INC_DIR}" "${LIB_DIR}/nfft3/include" "symlink"
+  else
+    echo "Fetching NFFT tarball for headers (${NFFT_VERSION})"
+    need_cmd tar
+    tar_name="nfft-${NFFT_VERSION}.tar.gz"
+    tar_path="${LIB_DIR}/${tar_name}"
+    url="http://www.nfft.org/download/${tar_name}"
+    fetch_tarball "${url}" "${tar_path}"
+    ( cd "${LIB_DIR}" && tar xzf "${tar_name}" )
+    rm -f "${LIB_DIR}/nfft3"
+    ln -s "nfft-${NFFT_VERSION}" "${LIB_DIR}/nfft3"
+  fi
+
+  echo
+  echo "Header checks (expected by src/Makefile):"
+  for f in \
+    "${LIB_DIR}/luajit/src/lua.h" \
+    "${LIB_DIR}/nlopt/src/api/nlopt.h" \
+    "${LIB_DIR}/fftw3/api/fftw3.h" \
+    "${LIB_DIR}/nfft3/include/nfft3.h"
+  do
+    if [[ -e "${f}" ]]; then
+      echo "  OK  ${f}"
+    else
+      echo "  MISS ${f}"
+    fi
+  done
+}
+
+main "$@"
+

From 37c98a3bb577b92bfefa221621d207a506405c18 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 21:31:59 +0200
Subject: [PATCH 04/69] Update NFFT download URL in staging scripts for Linux
 and macOS

---
 tools/stage_madng_headers_linux.sh | 3 +--
 tools/stage_madng_headers_macos.sh | 3 +--
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/tools/stage_madng_headers_linux.sh b/tools/stage_madng_headers_linux.sh
index c74534a..6b199d2 100755
--- a/tools/stage_madng_headers_linux.sh
+++ b/tools/stage_madng_headers_linux.sh
@@ -138,7 +138,7 @@ main() {
     need_cmd tar
     tar_name="nfft-${NFFT_VERSION}.tar.gz"
     tar_path="${LIB_DIR}/${tar_name}"
-    url="http://www.nfft.org/download/${tar_name}"
+    url="https://www-user.tu-chemnitz.de/~potts/nfft/download/${tar_name}"
     fetch_tarball "${url}" "${tar_path}"
     ( cd "${LIB_DIR}" && tar xzf "${tar_name}" )
     rm -f "${LIB_DIR}/nfft3"
@@ -162,4 +162,3 @@ main() {
 }
 
 main "$@"
-
diff --git a/tools/stage_madng_headers_macos.sh b/tools/stage_madng_headers_macos.sh
index 44f5b59..23fb440 100755
--- a/tools/stage_madng_headers_macos.sh
+++ b/tools/stage_madng_headers_macos.sh
@@ -138,7 +138,7 @@ main() {
     need_cmd tar
     tar_name="nfft-${NFFT_VERSION}.tar.gz"
     tar_path="${LIB_DIR}/${tar_name}"
-    url="http://www.nfft.org/download/${tar_name}"
+    url="https://www-user.tu-chemnitz.de/~potts/nfft/download/${tar_name}"
     fetch_tarball "${url}" "${tar_path}"
     ( cd "${LIB_DIR}" && tar xzf "${tar_name}" )
     rm -f "${LIB_DIR}/nfft3"
@@ -162,4 +162,3 @@ main() {
 }
 
 main "$@"
-

From ad14b967086e4ead7c07ea12918692ac15c0d758 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 21:38:34 +0200
Subject: [PATCH 05/69] Enhance header staging scripts for LuaJIT compatibility
 and update Makefile selection for macOS

---
 .github/workflows/compile_madng.yml | 16 +++++++++++++++-
 tools/stage_madng_headers_linux.sh  |  8 +++++++-
 tools/stage_madng_headers_macos.sh  |  8 +++++++-
 3 files changed, 29 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 297c1a0..a325ebb 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -34,6 +34,15 @@ jobs:
           cp MAD/src/Makefile.lxplus MAD/src/Makefile
         elif [ "$RUNNER_OS" = "macOS" ]; then
           cp MAD/src/Makefile.macosx MAD/src/Makefile
+
+          # Ensure we use Homebrew LLVM clang (Apple clang doesn't support -fopenmp)
+          brew_prefix_llvm="$(brew --prefix llvm)"
+          sed -i.bak \
+            -e "s#^CC[[:space:]]*=[[:space:]]*gcc#CC=${brew_prefix_llvm}/bin/clang#g" \
+            -e "s#^CC[[:space:]]*=[[:space:]]*clang#CC=${brew_prefix_llvm}/bin/clang#g" \
+            -e "s#^CXX[[:space:]]*=[[:space:]]*g\\+\\+#CXX=${brew_prefix_llvm}/bin/clang++#g" \
+            -e "s#^CXX[[:space:]]*=[[:space:]]*clang\\+\\+#CXX=${brew_prefix_llvm}/bin/clang++#g" \
+            MAD/src/Makefile
         else
           echo "Unsupported OS: $RUNNER_OS"
           exit 1
@@ -61,6 +70,7 @@ jobs:
         sudo apt-get update
         sudo apt-get install -y \
           build-essential \
+          clang \
           gcc \
           g++ \
           make \
@@ -75,6 +85,10 @@ jobs:
       working-directory: MAD/src
 
       run: |
+        if [ "$RUNNER_OS" = "Linux" ]; then
+          export CC=clang
+          export CXX=clang++
+        fi
         if [ "$RUNNER_OS" = "macOS" ]; then
           export PATH="$(brew --prefix llvm)/bin:$PATH"
           export CC="$(brew --prefix llvm)/bin/clang"
@@ -82,7 +96,7 @@ jobs:
           export CPPFLAGS="-I$(brew --prefix libomp)/include"
           export LDFLAGS="-L$(brew --prefix libomp)/lib -lomp"
         fi
-        make -j
+        make -j SHELL=/bin/bash
 
     - name: Upload it
       uses: actions/upload-artifact@v7
diff --git a/tools/stage_madng_headers_linux.sh b/tools/stage_madng_headers_linux.sh
index 6b199d2..0238cb6 100755
--- a/tools/stage_madng_headers_linux.sh
+++ b/tools/stage_madng_headers_linux.sh
@@ -4,7 +4,7 @@ set -euo pipefail
 # Stage headers into the layout expected by MAD-NG's unmodified `src/Makefile`.
 #
 # Expected include paths (from `src/Makefile`):
-#   -I../lib/luajit/src            -> lua.h, luaconf.h, lualib.h, lauxlib.h, lua.hpp
+#   -I../lib/luajit/src            -> lua.h, luajit.h, luaconf.h, lualib.h, lauxlib.h, lua.hpp
 #   -I../lib/nlopt/src/api         -> nlopt.h
 #   -I../lib/fftw3/api             -> fftw3.h
 #   -I../lib/nfft3/include         -> nfft3.h (and friends)
@@ -92,6 +92,11 @@ main() {
       git checkout "${LUAJIT_REF}"
       git pull --ff-only || true
     )
+
+    # Some LuaJIT variants ship `luajit.h.in` instead of `luajit.h`.
+    if [[ ! -e "${local_dir}/src/luajit.h" && -e "${local_dir}/src/luajit.h.in" ]]; then
+      cp -f "${local_dir}/src/luajit.h.in" "${local_dir}/src/luajit.h"
+    fi
   fi
 
   # NLOpt headers -> lib/nlopt/src/api/nlopt.h
@@ -149,6 +154,7 @@ main() {
   echo "Header checks (expected by src/Makefile):"
   for f in \
     "${LIB_DIR}/luajit/src/lua.h" \
+    "${LIB_DIR}/luajit/src/luajit.h" \
     "${LIB_DIR}/nlopt/src/api/nlopt.h" \
     "${LIB_DIR}/fftw3/api/fftw3.h" \
     "${LIB_DIR}/nfft3/include/nfft3.h"
diff --git a/tools/stage_madng_headers_macos.sh b/tools/stage_madng_headers_macos.sh
index 23fb440..a713ab7 100755
--- a/tools/stage_madng_headers_macos.sh
+++ b/tools/stage_madng_headers_macos.sh
@@ -4,7 +4,7 @@ set -euo pipefail
 # Stage headers into the layout expected by MAD-NG's unmodified `src/Makefile`.
 #
 # Expected include paths (from `src/Makefile`):
-#   -I../lib/luajit/src            -> lua.h etc
+#   -I../lib/luajit/src            -> lua.h, luajit.h, etc
 #   -I../lib/nlopt/src/api         -> nlopt.h
 #   -I../lib/fftw3/api             -> fftw3.h
 #   -I../lib/nfft3/include         -> nfft3.h
@@ -92,6 +92,11 @@ main() {
       git checkout "${LUAJIT_REF}"
       git pull --ff-only || true
     )
+
+    # Some LuaJIT variants ship `luajit.h.in` instead of `luajit.h`.
+    if [[ ! -e "${local_dir}/src/luajit.h" && -e "${local_dir}/src/luajit.h.in" ]]; then
+      cp -f "${local_dir}/src/luajit.h.in" "${local_dir}/src/luajit.h"
+    fi
   fi
 
   # NLOpt headers -> lib/nlopt/src/api/nlopt.h
@@ -149,6 +154,7 @@ main() {
   echo "Header checks (expected by src/Makefile):"
   for f in \
     "${LIB_DIR}/luajit/src/lua.h" \
+    "${LIB_DIR}/luajit/src/luajit.h" \
     "${LIB_DIR}/nlopt/src/api/nlopt.h" \
     "${LIB_DIR}/fftw3/api/fftw3.h" \
     "${LIB_DIR}/nfft3/include/nfft3.h"

From 39d673c0a2237f055b64897be308a4726d0351d0 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 21:46:28 +0200
Subject: [PATCH 06/69] Add fallback for luajit.h staging in Linux and macOS
 header scripts

---
 .github/workflows/compile_madng.yml | 9 ++++++++-
 tools/stage_madng_headers_linux.sh  | 8 ++++++++
 tools/stage_madng_headers_macos.sh  | 8 ++++++++
 3 files changed, 24 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index a325ebb..21bee66 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -32,6 +32,12 @@ jobs:
       run: |
         if [ "$RUNNER_OS" = "Linux" ]; then
           cp MAD/src/Makefile.lxplus MAD/src/Makefile
+
+          # Prefer clang/clang++ on CI (Makefile.lxplus may default to gcc/g++)
+          sed -i \
+            -e 's#^CC[[:space:]]*=.*#CC=clang#g' \
+            -e 's#^CXX[[:space:]]*=.*#CXX=clang++#g' \
+            MAD/src/Makefile || true
         elif [ "$RUNNER_OS" = "macOS" ]; then
           cp MAD/src/Makefile.macosx MAD/src/Makefile
 
@@ -96,7 +102,8 @@ jobs:
           export CPPFLAGS="-I$(brew --prefix libomp)/include"
           export LDFLAGS="-L$(brew --prefix libomp)/lib -lomp"
         fi
-        make -j SHELL=/bin/bash
+        # Enable job control for Makefile recipes that use `bg`
+        bash -m -lc "make -j CC='${CC}' CXX='${CXX}' CPPFLAGS='${CPPFLAGS:-}' LDFLAGS='${LDFLAGS:-}'"
 
     - name: Upload it
       uses: actions/upload-artifact@v7
diff --git a/tools/stage_madng_headers_linux.sh b/tools/stage_madng_headers_linux.sh
index 0238cb6..1efeb3d 100755
--- a/tools/stage_madng_headers_linux.sh
+++ b/tools/stage_madng_headers_linux.sh
@@ -97,6 +97,14 @@ main() {
     if [[ ! -e "${local_dir}/src/luajit.h" && -e "${local_dir}/src/luajit.h.in" ]]; then
       cp -f "${local_dir}/src/luajit.h.in" "${local_dir}/src/luajit.h"
     fi
+
+    # Fallback: some forks may place the template elsewhere.
+    if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
+      alt="$(find "${local_dir}" -maxdepth 3 -name 'luajit.h.in' -o -name 'luajit.h' | head -n 1 || true)"
+      if [[ -n "${alt}" && -e "${alt}" ]]; then
+        cp -f "${alt}" "${local_dir}/src/luajit.h"
+      fi
+    fi
   fi
 
   # NLOpt headers -> lib/nlopt/src/api/nlopt.h
diff --git a/tools/stage_madng_headers_macos.sh b/tools/stage_madng_headers_macos.sh
index a713ab7..eeac3fb 100755
--- a/tools/stage_madng_headers_macos.sh
+++ b/tools/stage_madng_headers_macos.sh
@@ -97,6 +97,14 @@ main() {
     if [[ ! -e "${local_dir}/src/luajit.h" && -e "${local_dir}/src/luajit.h.in" ]]; then
       cp -f "${local_dir}/src/luajit.h.in" "${local_dir}/src/luajit.h"
     fi
+
+    # Fallback: some forks may place the template elsewhere.
+    if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
+      alt="$(find "${local_dir}" -maxdepth 3 -name 'luajit.h.in' -o -name 'luajit.h' | head -n 1 || true)"
+      if [[ -n "${alt}" && -e "${alt}" ]]; then
+        cp -f "${alt}" "${local_dir}/src/luajit.h"
+      fi
+    fi
   fi
 
   # NLOpt headers -> lib/nlopt/src/api/nlopt.h

From e9e0cbd24ade2e4d89be75ae8fb4d7614aa740be Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 21:53:34 +0200
Subject: [PATCH 07/69] Refactor GitHub Actions workflow for MAD-NG binary
 compilation

---
 .github/workflows/compile_madng.yml | 99 ++++++++++++++---------------
 1 file changed, 46 insertions(+), 53 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 21bee66..03b4204 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -1,6 +1,3 @@
-# This workflow will install Python dependencies, run tests on a variety Python versions
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
 name: Make a MAD-NG Binary
 
 on:
@@ -19,94 +16,90 @@ jobs:
 
     steps:
     - name: Checkout current repo
-      uses: actions/checkout@v6
+      uses: actions/checkout@v4
 
-    - name: Clone another repo
-      uses: actions/checkout@v6
+    - name: Clone MAD-NG
+      uses: actions/checkout@v4
       with:
         repository: MethodicalAcceleratorDesign/MAD-NG
         path: MAD
         submodules: recursive
 
+    - name: Install dependencies
+      run: |
+        if [ "$RUNNER_OS" = "Linux" ]; then
+          sudo apt-get update
+          sudo apt-get install -y build-essential
+        elif [ "$RUNNER_OS" = "macOS" ]; then
+          brew update
+          brew install llvm libomp
+        fi
+
     - name: Select Makefile
       run: |
         if [ "$RUNNER_OS" = "Linux" ]; then
           cp MAD/src/Makefile.lxplus MAD/src/Makefile
-
-          # Prefer clang/clang++ on CI (Makefile.lxplus may default to gcc/g++)
           sed -i \
-            -e 's#^CC[[:space:]]*=.*#CC=clang#g' \
-            -e 's#^CXX[[:space:]]*=.*#CXX=clang++#g' \
+            -e 's#^CC[[:space:]]*=.*#CC=gcc#g' \
+            -e 's#^CXX[[:space:]]*=.*#CXX=g++#g' \
+            -e 's#-fdiagnostics-all-candidates##g' \
             MAD/src/Makefile || true
         elif [ "$RUNNER_OS" = "macOS" ]; then
-          cp MAD/src/Makefile.macosx MAD/src/Makefile
-
-          # Ensure we use Homebrew LLVM clang (Apple clang doesn't support -fopenmp)
           brew_prefix_llvm="$(brew --prefix llvm)"
+          cp MAD/src/Makefile.macosx MAD/src/Makefile
           sed -i.bak \
             -e "s#^CC[[:space:]]*=[[:space:]]*gcc#CC=${brew_prefix_llvm}/bin/clang#g" \
             -e "s#^CC[[:space:]]*=[[:space:]]*clang#CC=${brew_prefix_llvm}/bin/clang#g" \
             -e "s#^CXX[[:space:]]*=[[:space:]]*g\\+\\+#CXX=${brew_prefix_llvm}/bin/clang++#g" \
             -e "s#^CXX[[:space:]]*=[[:space:]]*clang\\+\\+#CXX=${brew_prefix_llvm}/bin/clang++#g" \
+            -e "s#-fdiagnostics-all-candidates##g" \
             MAD/src/Makefile
-        else
-          echo "Unsupported OS: $RUNNER_OS"
-          exit 1
         fi
 
     - name: Stage MAD-NG headers
       run: |
         mkdir -p MAD/tools
-        cp -f tools/stage_madng_headers_linux.sh MAD/tools/ || true
-        cp -f tools/stage_madng_headers_macos.sh MAD/tools/ || true
-        chmod +x MAD/tools/stage_madng_headers_*.sh
-
         if [ "$RUNNER_OS" = "Linux" ]; then
+          cp -f tools/stage_madng_headers_linux.sh MAD/tools/
+          chmod +x MAD/tools/stage_madng_headers_linux.sh
           (cd MAD && ./tools/stage_madng_headers_linux.sh)
         elif [ "$RUNNER_OS" = "macOS" ]; then
+          cp -f tools/stage_madng_headers_macos.sh MAD/tools/
+          chmod +x MAD/tools/stage_madng_headers_macos.sh
           (cd MAD && ./tools/stage_madng_headers_macos.sh)
-        else
-          echo "Unsupported OS: $RUNNER_OS"
-          exit 1
         fi
 
-    - name: Install Linux dependencies
-      if: runner.os == 'Linux'
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y \
-          build-essential \
-          clang \
-          gcc \
-          g++ \
-          make \
-
-    - name: Install macOS dependencies
-      if: runner.os == 'macOS'
-      run: |
-        brew update
-        brew install llvm libomp
-
     - name: Compile MAD-NG
       working-directory: MAD/src
-
       run: |
+        # GitHub Actions has no TTY/job-control; provide a synchronous `bg` shim.
+        mkdir -p "${RUNNER_TEMP}/madng-bin"
+        printf '#!/usr/bin/env bash\n[ "$#" -ge 2 ] && "$1" > "$2"\n' \
+          > "${RUNNER_TEMP}/madng-bin/bg"
+        chmod +x "${RUNNER_TEMP}/madng-bin/bg"
+        export PATH="${RUNNER_TEMP}/madng-bin:${PATH}"
+
         if [ "$RUNNER_OS" = "Linux" ]; then
-          export CC=clang
-          export CXX=clang++
-        fi
-        if [ "$RUNNER_OS" = "macOS" ]; then
-          export PATH="$(brew --prefix llvm)/bin:$PATH"
-          export CC="$(brew --prefix llvm)/bin/clang"
-          export CXX="$(brew --prefix llvm)/bin/clang++"
+          export CC=gcc CXX=g++
+        elif [ "$RUNNER_OS" = "macOS" ]; then
+          llvm="$(brew --prefix llvm)"
+          export PATH="${llvm}/bin:${PATH}"
+          export CC="${llvm}/bin/clang" CXX="${llvm}/bin/clang++"
           export CPPFLAGS="-I$(brew --prefix libomp)/include"
           export LDFLAGS="-L$(brew --prefix libomp)/lib -lomp"
+          # Avoid x86_64-specific tuning flags on arm64.
+          export CFLAGS="-O3 -ftree-vectorize -fPIC -flto"
+          export CXXFLAGS="-O3 -ftree-vectorize -fPIC -flto"
         fi
-        # Enable job control for Makefile recipes that use `bg`
-        bash -m -lc "make -j CC='${CC}' CXX='${CXX}' CPPFLAGS='${CPPFLAGS:-}' LDFLAGS='${LDFLAGS:-}'"
 
-    - name: Upload it
-      uses: actions/upload-artifact@v7
+        JOBS=$(nproc 2>/dev/null || sysctl -n hw.logicalcpu)
+        make -j"${JOBS}" SHELL=/bin/bash \
+          CC="${CC}" CXX="${CXX}" \
+          CPPFLAGS="${CPPFLAGS:-}" LDFLAGS="${LDFLAGS:-}" \
+          CFLAGS="${CFLAGS:-}" CXXFLAGS="${CXXFLAGS:-}"
+
+    - name: Upload binary
+      uses: actions/upload-artifact@v4
       with:
-        name: executable-${{ runner.os }}
+        name: mad-${{ runner.os }}
         path: MAD/src/mad

From 0ab8ca231b53f1fdb59355d1d7e3022d1a3adfda Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 22:01:26 +0200
Subject: [PATCH 08/69] Add error handling for missing headers in staging
 scripts for Linux and macOS

---
 tools/stage_madng_headers_linux.sh | 5 ++++-
 tools/stage_madng_headers_macos.sh | 5 ++++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/tools/stage_madng_headers_linux.sh b/tools/stage_madng_headers_linux.sh
index 1efeb3d..81eebd2 100755
--- a/tools/stage_madng_headers_linux.sh
+++ b/tools/stage_madng_headers_linux.sh
@@ -160,6 +160,7 @@ main() {
 
   echo
   echo "Header checks (expected by src/Makefile):"
+  local rc=0
   for f in \
     "${LIB_DIR}/luajit/src/lua.h" \
     "${LIB_DIR}/luajit/src/luajit.h" \
@@ -170,9 +171,11 @@ main() {
     if [[ -e "${f}" ]]; then
       echo "  OK  ${f}"
     else
-      echo "  MISS ${f}"
+      echo "  MISS ${f}" >&2
+      rc=1
     fi
   done
+  return "${rc}"
 }
 
 main "$@"
diff --git a/tools/stage_madng_headers_macos.sh b/tools/stage_madng_headers_macos.sh
index eeac3fb..ab19f85 100755
--- a/tools/stage_madng_headers_macos.sh
+++ b/tools/stage_madng_headers_macos.sh
@@ -160,6 +160,7 @@ main() {
 
   echo
   echo "Header checks (expected by src/Makefile):"
+  local rc=0
   for f in \
     "${LIB_DIR}/luajit/src/lua.h" \
     "${LIB_DIR}/luajit/src/luajit.h" \
@@ -170,9 +171,11 @@ main() {
     if [[ -e "${f}" ]]; then
       echo "  OK  ${f}"
     else
-      echo "  MISS ${f}"
+      echo "  MISS ${f}" >&2
+      rc=1
     fi
   done
+  return "${rc}"
 }
 
 main "$@"

From 756630c50908a860b782a5d8ba18c9c2a26d3657 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 22:04:38 +0200
Subject: [PATCH 09/69] Add fallback to generate luajit.h during build in
 staging scripts for Linux and macOS

---
 tools/stage_madng_headers_linux.sh | 10 +++++++++-
 tools/stage_madng_headers_macos.sh | 10 +++++++++-
 2 files changed, 18 insertions(+), 2 deletions(-)

diff --git a/tools/stage_madng_headers_linux.sh b/tools/stage_madng_headers_linux.sh
index 81eebd2..dca2931 100755
--- a/tools/stage_madng_headers_linux.sh
+++ b/tools/stage_madng_headers_linux.sh
@@ -100,11 +100,19 @@ main() {
 
     # Fallback: some forks may place the template elsewhere.
     if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
-      alt="$(find "${local_dir}" -maxdepth 3 -name 'luajit.h.in' -o -name 'luajit.h' | head -n 1 || true)"
+      alt="$(find "${local_dir}" -maxdepth 3 \( -name 'luajit.h.in' -o -name 'luajit.h' \) | head -n 1 || true)"
       if [[ -n "${alt}" && -e "${alt}" ]]; then
         cp -f "${alt}" "${local_dir}/src/luajit.h"
       fi
     fi
+
+    # Last resort: the MAD-patch fork generates luajit.h during build.
+    if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
+      echo "luajit.h not in repo — generating via make..."
+      make -C "${local_dir}/src" luajit.h 2>/dev/null \
+        || make -C "${local_dir}" 2>/dev/null \
+        || true
+    fi
   fi
 
   # NLOpt headers -> lib/nlopt/src/api/nlopt.h
diff --git a/tools/stage_madng_headers_macos.sh b/tools/stage_madng_headers_macos.sh
index ab19f85..5c15779 100755
--- a/tools/stage_madng_headers_macos.sh
+++ b/tools/stage_madng_headers_macos.sh
@@ -100,11 +100,19 @@ main() {
 
     # Fallback: some forks may place the template elsewhere.
     if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
-      alt="$(find "${local_dir}" -maxdepth 3 -name 'luajit.h.in' -o -name 'luajit.h' | head -n 1 || true)"
+      alt="$(find "${local_dir}" -maxdepth 3 \( -name 'luajit.h.in' -o -name 'luajit.h' \) | head -n 1 || true)"
       if [[ -n "${alt}" && -e "${alt}" ]]; then
         cp -f "${alt}" "${local_dir}/src/luajit.h"
       fi
     fi
+
+    # Last resort: the MAD-patch fork generates luajit.h during build.
+    if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
+      echo "luajit.h not in repo — generating via make..."
+      make -C "${local_dir}/src" luajit.h 2>/dev/null \
+        || make -C "${local_dir}" 2>/dev/null \
+        || true
+    fi
   fi
 
   # NLOpt headers -> lib/nlopt/src/api/nlopt.h

From 02a07e3a85751d66cecc08badab35fb53c130504 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 22:08:34 +0200
Subject: [PATCH 10/69] Add library include paths for LuaJIT and other
 dependencies in compilation scripts

---
 .github/workflows/compile_madng.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 03b4204..e60bdb2 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -79,13 +79,17 @@ jobs:
         chmod +x "${RUNNER_TEMP}/madng-bin/bg"
         export PATH="${RUNNER_TEMP}/madng-bin:${PATH}"
 
+        # Include paths the Makefile expects to find in ../lib relative to src/.
+        LIB_INCLUDES="-I../lib/luajit/src -I../lib/nlopt/src/api -I../lib/fftw3/api -I../lib/nfft3/include"
+
         if [ "$RUNNER_OS" = "Linux" ]; then
           export CC=gcc CXX=g++
+          export CPPFLAGS="${LIB_INCLUDES}"
         elif [ "$RUNNER_OS" = "macOS" ]; then
           llvm="$(brew --prefix llvm)"
           export PATH="${llvm}/bin:${PATH}"
           export CC="${llvm}/bin/clang" CXX="${llvm}/bin/clang++"
-          export CPPFLAGS="-I$(brew --prefix libomp)/include"
+          export CPPFLAGS="${LIB_INCLUDES} -I$(brew --prefix libomp)/include"
           export LDFLAGS="-L$(brew --prefix libomp)/lib -lomp"
           # Avoid x86_64-specific tuning flags on arm64.
           export CFLAGS="-O3 -ftree-vectorize -fPIC -flto"

From f578ad1a814cb673afe22d175c3fef4c88580b18 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 22:13:34 +0200
Subject: [PATCH 11/69] Update include paths to absolute references in Makefile
 for compatibility with sub-processes

---
 .github/workflows/compile_madng.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index e60bdb2..906db3a 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -79,8 +79,9 @@ jobs:
         chmod +x "${RUNNER_TEMP}/madng-bin/bg"
         export PATH="${RUNNER_TEMP}/madng-bin:${PATH}"
 
-        # Include paths the Makefile expects to find in ../lib relative to src/.
-        LIB_INCLUDES="-I../lib/luajit/src -I../lib/nlopt/src/api -I../lib/fftw3/api -I../lib/nfft3/include"
+        # Absolute include paths — relative ones break when make spawns sub-processes.
+        LIB="$(cd ../lib && pwd)"
+        LIB_INCLUDES="-I${LIB}/luajit/src -I${LIB}/nlopt/src/api -I${LIB}/fftw3/api -I${LIB}/nfft3/include"
 
         if [ "$RUNNER_OS" = "Linux" ]; then
           export CC=gcc CXX=g++

From 10cf1a8a0d2455a98e60289a3cd6a4a332f59596 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 22:18:37 +0200
Subject: [PATCH 12/69] Refactor Makefile selection and compilation steps for
 improved compatibility and clarity

---
 .github/workflows/compile_madng.yml | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 906db3a..1041343 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -53,6 +53,9 @@ jobs:
             -e "s#^CXX[[:space:]]*=[[:space:]]*g\\+\\+#CXX=${brew_prefix_llvm}/bin/clang++#g" \
             -e "s#^CXX[[:space:]]*=[[:space:]]*clang\\+\\+#CXX=${brew_prefix_llvm}/bin/clang++#g" \
             -e "s#-fdiagnostics-all-candidates##g" \
+            -e "s#-march=native##g" \
+            -e "s#-mtune=native##g" \
+            -e "s#-mfma##g" \
             MAD/src/Makefile
         fi
 
@@ -82,26 +85,27 @@ jobs:
         # Absolute include paths — relative ones break when make spawns sub-processes.
         LIB="$(cd ../lib && pwd)"
         LIB_INCLUDES="-I${LIB}/luajit/src -I${LIB}/nlopt/src/api -I${LIB}/fftw3/api -I${LIB}/nfft3/include"
+        COMMON_CFLAGS="${LIB_INCLUDES}"
 
         if [ "$RUNNER_OS" = "Linux" ]; then
           export CC=gcc CXX=g++
-          export CPPFLAGS="${LIB_INCLUDES}"
+          # MAD-NG Makefiles typically use CFLAGS for include paths.
+          export CFLAGS="${COMMON_CFLAGS}"
+          export CXXFLAGS="${COMMON_CFLAGS}"
         elif [ "$RUNNER_OS" = "macOS" ]; then
           llvm="$(brew --prefix llvm)"
           export PATH="${llvm}/bin:${PATH}"
           export CC="${llvm}/bin/clang" CXX="${llvm}/bin/clang++"
-          export CPPFLAGS="${LIB_INCLUDES} -I$(brew --prefix libomp)/include"
+          export CFLAGS="${COMMON_CFLAGS} -I$(brew --prefix libomp)/include"
+          export CXXFLAGS="${CFLAGS}"
           export LDFLAGS="-L$(brew --prefix libomp)/lib -lomp"
-          # Avoid x86_64-specific tuning flags on arm64.
-          export CFLAGS="-O3 -ftree-vectorize -fPIC -flto"
-          export CXXFLAGS="-O3 -ftree-vectorize -fPIC -flto"
         fi
 
         JOBS=$(nproc 2>/dev/null || sysctl -n hw.logicalcpu)
         make -j"${JOBS}" SHELL=/bin/bash \
           CC="${CC}" CXX="${CXX}" \
-          CPPFLAGS="${CPPFLAGS:-}" LDFLAGS="${LDFLAGS:-}" \
-          CFLAGS="${CFLAGS:-}" CXXFLAGS="${CXXFLAGS:-}"
+          CFLAGS="${CFLAGS:-}" CXXFLAGS="${CXXFLAGS:-}" \
+          LDFLAGS="${LDFLAGS:-}"
 
     - name: Upload binary
       uses: actions/upload-artifact@v4

From 84523862e3bdaebe0de8beaa91230f496c619b4d Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 22:23:37 +0200
Subject: [PATCH 13/69] Enhance MAD-NG compilation process by adding a
 synchronous bg shim and refining include path handling for improved
 compatibility

---
 .github/workflows/compile_madng.yml | 34 ++++++++++++++++++-----------
 1 file changed, 21 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 1041343..d20b826 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -75,29 +75,37 @@ jobs:
     - name: Compile MAD-NG
       working-directory: MAD/src
       run: |
-        # GitHub Actions has no TTY/job-control; provide a synchronous `bg` shim.
-        mkdir -p "${RUNNER_TEMP}/madng-bin"
-        printf '#!/usr/bin/env bash\n[ "$#" -ge 2 ] && "$1" > "$2"\n' \
-          > "${RUNNER_TEMP}/madng-bin/bg"
-        chmod +x "${RUNNER_TEMP}/madng-bin/bg"
-        export PATH="${RUNNER_TEMP}/madng-bin:${PATH}"
+        # GitHub Actions has no job control/TTY. MAD-NG Makefiles use `bg ...`
+        # to parallelize some conversions; patch it to run synchronously.
+        sed -i.bak -e 's#^bg #./bg_shim #g' Makefile || true
 
-        # Absolute include paths — relative ones break when make spawns sub-processes.
+        printf '%s\n' \
+          '#!/usr/bin/env bash' \
+          'set -euo pipefail' \
+          '# expected: bg <script> <output>' \
+          'script="${1:-}"' \
+          'out="${2:-}"' \
+          'if [[ -z "${script}" || -z "${out}" ]]; then' \
+          '  exit 0' \
+          'fi' \
+          '"${script}" > "${out}"' \
+          > ./bg_shim
+        chmod +x ./bg_shim
+
+        # Absolute include paths.
         LIB="$(cd ../lib && pwd)"
         LIB_INCLUDES="-I${LIB}/luajit/src -I${LIB}/nlopt/src/api -I${LIB}/fftw3/api -I${LIB}/nfft3/include"
-        COMMON_CFLAGS="${LIB_INCLUDES}"
 
         if [ "$RUNNER_OS" = "Linux" ]; then
           export CC=gcc CXX=g++
-          # MAD-NG Makefiles typically use CFLAGS for include paths.
-          export CFLAGS="${COMMON_CFLAGS}"
-          export CXXFLAGS="${COMMON_CFLAGS}"
+          export CFLAGS="${CFLAGS:-} ${LIB_INCLUDES}"
+          export CXXFLAGS="${CXXFLAGS:-} ${LIB_INCLUDES}"
         elif [ "$RUNNER_OS" = "macOS" ]; then
           llvm="$(brew --prefix llvm)"
           export PATH="${llvm}/bin:${PATH}"
           export CC="${llvm}/bin/clang" CXX="${llvm}/bin/clang++"
-          export CFLAGS="${COMMON_CFLAGS} -I$(brew --prefix libomp)/include"
-          export CXXFLAGS="${CFLAGS}"
+          export CFLAGS="${CFLAGS:-} ${LIB_INCLUDES} -I$(brew --prefix libomp)/include"
+          export CXXFLAGS="${CXXFLAGS:-} ${LIB_INCLUDES} -I$(brew --prefix libomp)/include"
           export LDFLAGS="-L$(brew --prefix libomp)/lib -lomp"
         fi
 

From 2f19b276222c41623f582830eaf189fcb57946f4 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 22:30:13 +0200
Subject: [PATCH 14/69] Update C++ compilation flags to enforce C++17 standard
 and permissive mode for improved compatibility

---
 .github/workflows/compile_madng.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index d20b826..161fb56 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -99,13 +99,13 @@ jobs:
         if [ "$RUNNER_OS" = "Linux" ]; then
           export CC=gcc CXX=g++
           export CFLAGS="${CFLAGS:-} ${LIB_INCLUDES}"
-          export CXXFLAGS="${CXXFLAGS:-} ${LIB_INCLUDES}"
+          export CXXFLAGS="${CXXFLAGS:-} -std=c++17 -fpermissive ${LIB_INCLUDES}"
         elif [ "$RUNNER_OS" = "macOS" ]; then
           llvm="$(brew --prefix llvm)"
           export PATH="${llvm}/bin:${PATH}"
           export CC="${llvm}/bin/clang" CXX="${llvm}/bin/clang++"
           export CFLAGS="${CFLAGS:-} ${LIB_INCLUDES} -I$(brew --prefix libomp)/include"
-          export CXXFLAGS="${CXXFLAGS:-} ${LIB_INCLUDES} -I$(brew --prefix libomp)/include"
+          export CXXFLAGS="${CXXFLAGS:-} -std=c++17 -fpermissive ${LIB_INCLUDES} -I$(brew --prefix libomp)/include"
           export LDFLAGS="-L$(brew --prefix libomp)/lib -lomp"
         fi
 

From bb8560fe735b5b0d0e6a57eed5cd1ffeca4ed881 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 22:45:08 +0200
Subject: [PATCH 15/69] Update compilation settings in workflow for improved
 compatibility with GCC 11 and Clang

---
 .github/workflows/compile_madng.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 161fb56..ffd8091 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -29,7 +29,7 @@ jobs:
       run: |
         if [ "$RUNNER_OS" = "Linux" ]; then
           sudo apt-get update
-          sudo apt-get install -y build-essential
+          sudo apt-get install -y build-essential gcc-11 g++-11
         elif [ "$RUNNER_OS" = "macOS" ]; then
           brew update
           brew install llvm libomp
@@ -40,8 +40,8 @@ jobs:
         if [ "$RUNNER_OS" = "Linux" ]; then
           cp MAD/src/Makefile.lxplus MAD/src/Makefile
           sed -i \
-            -e 's#^CC[[:space:]]*=.*#CC=gcc#g' \
-            -e 's#^CXX[[:space:]]*=.*#CXX=g++#g' \
+            -e 's#^CC[[:space:]]*=.*#CC=gcc-11#g' \
+            -e 's#^CXX[[:space:]]*=.*#CXX=g++-11#g' \
             -e 's#-fdiagnostics-all-candidates##g' \
             MAD/src/Makefile || true
         elif [ "$RUNNER_OS" = "macOS" ]; then
@@ -97,15 +97,15 @@ jobs:
         LIB_INCLUDES="-I${LIB}/luajit/src -I${LIB}/nlopt/src/api -I${LIB}/fftw3/api -I${LIB}/nfft3/include"
 
         if [ "$RUNNER_OS" = "Linux" ]; then
-          export CC=gcc CXX=g++
+          export CC=gcc-11 CXX=g++-11
           export CFLAGS="${CFLAGS:-} ${LIB_INCLUDES}"
-          export CXXFLAGS="${CXXFLAGS:-} -std=c++17 -fpermissive ${LIB_INCLUDES}"
+          export CXXFLAGS="${CXXFLAGS:-} -std=c++17 ${LIB_INCLUDES}"
         elif [ "$RUNNER_OS" = "macOS" ]; then
           llvm="$(brew --prefix llvm)"
           export PATH="${llvm}/bin:${PATH}"
           export CC="${llvm}/bin/clang" CXX="${llvm}/bin/clang++"
           export CFLAGS="${CFLAGS:-} ${LIB_INCLUDES} -I$(brew --prefix libomp)/include"
-          export CXXFLAGS="${CXXFLAGS:-} -std=c++17 -fpermissive ${LIB_INCLUDES} -I$(brew --prefix libomp)/include"
+          export CXXFLAGS="${CXXFLAGS:-} -std=c++17 ${LIB_INCLUDES} -I$(brew --prefix libomp)/include"
           export LDFLAGS="-L$(brew --prefix libomp)/lib -lomp"
         fi
 

From b3e361c9a68bd5de1e1f134803c5e1e8b6e7f50c Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 22:49:24 +0200
Subject: [PATCH 16/69] more edits

---
 .github/workflows/compile_madng.yml | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index ffd8091..1eaa324 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -109,6 +109,19 @@ jobs:
           export LDFLAGS="-L$(brew --prefix libomp)/lib -lomp"
         fi
 
+        # Patch template syntax errors in mad_dynmap.cpp for GitHub Actions runner.
+        # Adding 'typename' fixes C++ standard compliance without changing functionality.
+        # Only patches the cloned copy in CI, not upstream.
+        if [ -f mad_dynmap.cpp ]; then
+          sed -i.bak \
+            -e 's/M::MT/typename M::MT/g' \
+            -e 's/M::MP/typename M::MP/g' \
+            -e 's/M::T/typename M::T/g' \
+            -e 's/M::P/typename M::P/g' \
+            -e 's/M::R/typename M::R/g' \
+            mad_dynmap.cpp || true
+        fi
+
         JOBS=$(nproc 2>/dev/null || sysctl -n hw.logicalcpu)
         make -j"${JOBS}" SHELL=/bin/bash \
           CC="${CC}" CXX="${CXX}" \

From b9b152e0992291a189304149ac5d5001049b65db Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 23:01:36 +0200
Subject: [PATCH 17/69] Refactor MAD-NG compilation to remove 'bg' commands for
 sequential execution and improve compatibility with GitHub Actions

---
 .github/workflows/compile_madng.yml | 23 ++++-------------------
 1 file changed, 4 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 1eaa324..8bff81a 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -75,23 +75,6 @@ jobs:
     - name: Compile MAD-NG
       working-directory: MAD/src
       run: |
-        # GitHub Actions has no job control/TTY. MAD-NG Makefiles use `bg ...`
-        # to parallelize some conversions; patch it to run synchronously.
-        sed -i.bak -e 's#^bg #./bg_shim #g' Makefile || true
-
-        printf '%s\n' \
-          '#!/usr/bin/env bash' \
-          'set -euo pipefail' \
-          '# expected: bg <script> <output>' \
-          'script="${1:-}"' \
-          'out="${2:-}"' \
-          'if [[ -z "${script}" || -z "${out}" ]]; then' \
-          '  exit 0' \
-          'fi' \
-          '"${script}" > "${out}"' \
-          > ./bg_shim
-        chmod +x ./bg_shim
-
         # Absolute include paths.
         LIB="$(cd ../lib && pwd)"
         LIB_INCLUDES="-I${LIB}/luajit/src -I${LIB}/nlopt/src/api -I${LIB}/fftw3/api -I${LIB}/nfft3/include"
@@ -109,6 +92,9 @@ jobs:
           export LDFLAGS="-L$(brew --prefix libomp)/lib -lomp"
         fi
 
+        # Remove 'bg' commands from Makefile entirely (convert to sequential execution)
+        sed -i.bak -e 's#^bg \(.*\) \([^ ]*\)$#\1 > \2#g' Makefile || true
+
         # Patch template syntax errors in mad_dynmap.cpp for GitHub Actions runner.
         # Adding 'typename' fixes C++ standard compliance without changing functionality.
         # Only patches the cloned copy in CI, not upstream.
@@ -122,8 +108,7 @@ jobs:
             mad_dynmap.cpp || true
         fi
 
-        JOBS=$(nproc 2>/dev/null || sysctl -n hw.logicalcpu)
-        make -j"${JOBS}" SHELL=/bin/bash \
+        make SHELL=/bin/bash \
           CC="${CC}" CXX="${CXX}" \
           CFLAGS="${CFLAGS:-}" CXXFLAGS="${CXXFLAGS:-}" \
           LDFLAGS="${LDFLAGS:-}"

From aad88a422227d780c2c9872f2fda40cc24cda582 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 23:14:39 +0200
Subject: [PATCH 18/69] Refactor header staging scripts to improve luajit.h
 generation and suppress error output during git operations

---
 .github/workflows/compile_madng.yml |  3 ++-
 tools/stage_madng_headers_linux.sh  | 15 +++++++++++----
 tools/stage_madng_headers_macos.sh  | 15 +++++++++++----
 3 files changed, 24 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 8bff81a..9195ae5 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -93,7 +93,8 @@ jobs:
         fi
 
         # Remove 'bg' commands from Makefile entirely (convert to sequential execution)
-        sed -i.bak -e 's#^bg \(.*\) \([^ ]*\)$#\1 > \2#g' Makefile || true
+        # Handle tabs/spaces at line start and between arguments
+        sed -i.bak -E 's/^[[:space:]]*bg[[:space:]]+(.+)[[:space:]]+([^ ]+)$/\1 > \2/' Makefile || true
 
         # Patch template syntax errors in mad_dynmap.cpp for GitHub Actions runner.
         # Adding 'typename' fixes C++ standard compliance without changing functionality.
diff --git a/tools/stage_madng_headers_linux.sh b/tools/stage_madng_headers_linux.sh
index dca2931..12409ba 100755
--- a/tools/stage_madng_headers_linux.sh
+++ b/tools/stage_madng_headers_linux.sh
@@ -109,9 +109,16 @@ main() {
     # Last resort: the MAD-patch fork generates luajit.h during build.
     if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
       echo "luajit.h not in repo — generating via make..."
-      make -C "${local_dir}/src" luajit.h 2>/dev/null \
-        || make -C "${local_dir}" 2>/dev/null \
-        || true
+      ( cd "${local_dir}/src"
+        make luajit.h 2>/dev/null || true
+      )
+      if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
+        # Fallback: try building minilua and running it manually if make target fails
+        make -C "${local_dir}/src" host/minilua 2>/dev/null || true
+        if [[ -x "${local_dir}/src/host/minilua" ]]; then
+          "${local_dir}/src/host/minilua" "${local_dir}/src/genversion.lua" > "${local_dir}/src/luajit.h" 2>/dev/null || true
+        fi
+      fi
     fi
   fi
 
@@ -129,7 +136,7 @@ main() {
     ( cd "${local_dir}"
       git fetch --all --tags
       git checkout "${NLOPT_REF}"
-      git pull --ff-only || true
+      git pull --ff-only 2>/dev/null || true
     )
   fi
 
diff --git a/tools/stage_madng_headers_macos.sh b/tools/stage_madng_headers_macos.sh
index 5c15779..16d051a 100755
--- a/tools/stage_madng_headers_macos.sh
+++ b/tools/stage_madng_headers_macos.sh
@@ -109,9 +109,16 @@ main() {
     # Last resort: the MAD-patch fork generates luajit.h during build.
     if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
       echo "luajit.h not in repo — generating via make..."
-      make -C "${local_dir}/src" luajit.h 2>/dev/null \
-        || make -C "${local_dir}" 2>/dev/null \
-        || true
+      ( cd "${local_dir}/src"
+        make luajit.h 2>/dev/null || true
+      )
+      if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
+        # macOS: try building minilua and running it manually if make target fails
+        make -C "${local_dir}/src" host/minilua 2>/dev/null || true
+        if [[ -x "${local_dir}/src/host/minilua" ]]; then
+          "${local_dir}/src/host/minilua" "${local_dir}/src/genversion.lua" > "${local_dir}/src/luajit.h" 2>/dev/null || true
+        fi
+      fi
     fi
   fi
 
@@ -129,7 +136,7 @@ main() {
     ( cd "${local_dir}"
       git fetch --all --tags
       git checkout "${NLOPT_REF}"
-      git pull --ff-only || true
+      git pull --ff-only 2>/dev/null || true
     )
   fi
 

From 6f26e6e8a28fd91e7d2cd82ec5fb69ccafda58c9 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 23:20:52 +0200
Subject: [PATCH 19/69] Remove 'bg' commands from Makefile for sequential
 execution and add verification step

---
 .github/workflows/compile_madng.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 9195ae5..c7463f4 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -93,8 +93,12 @@ jobs:
         fi
 
         # Remove 'bg' commands from Makefile entirely (convert to sequential execution)
-        # Handle tabs/spaces at line start and between arguments
-        sed -i.bak -E 's/^[[:space:]]*bg[[:space:]]+(.+)[[:space:]]+([^ ]+)$/\1 > \2/' Makefile || true
+        # Pattern: match any line with 'bg input output' and replace with 'input > output'
+        sed -i.bak 's/^.*bg \([^ ]*\) \([^ ]*\)$/\1 > \2/' Makefile
+
+        # Verify the sed worked by checking a few lines
+        echo "=== Makefile after bg removal ==="
+        grep -c "^[^#]*bg " Makefile && echo "WARNING: bg commands still present!" || echo "OK: bg commands removed"
 
         # Patch template syntax errors in mad_dynmap.cpp for GitHub Actions runner.
         # Adding 'typename' fixes C++ standard compliance without changing functionality.

From 4e166a471dfc16d3829c254a312a6f5dd20ebbc6 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 23:23:39 +0200
Subject: [PATCH 20/69] Refactor Makefile to remove 'bg' commands for
 sequential execution and preserve indentation

---
 .github/workflows/compile_madng.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index c7463f4..2d39a65 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -93,8 +93,8 @@ jobs:
         fi
 
         # Remove 'bg' commands from Makefile entirely (convert to sequential execution)
-        # Pattern: match any line with 'bg input output' and replace with 'input > output'
-        sed -i.bak 's/^.*bg \([^ ]*\) \([^ ]*\)$/\1 > \2/' Makefile
+        # Preserve leading recipe indentation so Makefile separators remain valid.
+        sed -i.bak -E 's/^([[:space:]]*)bg[[:space:]]+([^[:space:]]+)[[:space:]]+([^[:space:]]+)$/\1\2 > \3/' Makefile
 
         # Verify the sed worked by checking a few lines
         echo "=== Makefile after bg removal ==="

From 11c757d0db131a5cf1137cccf3876ebfd1fcb400 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 23:27:51 +0200
Subject: [PATCH 21/69] Refactor build scripts to use 'make' or 'gmake' based
 on availability for header generation

---
 .github/workflows/compile_madng.yml |  2 +-
 tools/stage_madng_headers_linux.sh  | 16 +++++++++++++---
 tools/stage_madng_headers_macos.sh  | 14 ++++++++++++--
 3 files changed, 26 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 2d39a65..1431d84 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -32,7 +32,7 @@ jobs:
           sudo apt-get install -y build-essential gcc-11 g++-11
         elif [ "$RUNNER_OS" = "macOS" ]; then
           brew update
-          brew install llvm libomp
+          brew install llvm libomp make
         fi
 
     - name: Select Makefile
diff --git a/tools/stage_madng_headers_linux.sh b/tools/stage_madng_headers_linux.sh
index 12409ba..3c5a405 100755
--- a/tools/stage_madng_headers_linux.sh
+++ b/tools/stage_madng_headers_linux.sh
@@ -34,6 +34,14 @@ need_cmd() {
   command -v "$1" >/dev/null 2>&1 || { echo "Missing command: $1" >&2; exit 1; }
 }
 
+pick_make() {
+  if command -v gmake >/dev/null 2>&1; then
+    echo "gmake"
+  else
+    echo "make"
+  fi
+}
+
 fetch_tarball() {
   local url="$1"
   local out="$2"
@@ -100,7 +108,7 @@ main() {
 
     # Fallback: some forks may place the template elsewhere.
     if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
-      alt="$(find "${local_dir}" -maxdepth 3 \( -name 'luajit.h.in' -o -name 'luajit.h' \) | head -n 1 || true)"
+      alt="$(find "${local_dir}" -maxdepth 6 \( -name 'luajit.h.in' -o -name 'luajit.h' \) | head -n 1 || true)"
       if [[ -n "${alt}" && -e "${alt}" ]]; then
         cp -f "${alt}" "${local_dir}/src/luajit.h"
       fi
@@ -109,12 +117,14 @@ main() {
     # Last resort: the MAD-patch fork generates luajit.h during build.
     if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
       echo "luajit.h not in repo — generating via make..."
+      mk="$(pick_make)"
       ( cd "${local_dir}/src"
-        make luajit.h 2>/dev/null || true
+        "${mk}" luajit.h 2>/dev/null || true
       )
       if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
         # Fallback: try building minilua and running it manually if make target fails
-        make -C "${local_dir}/src" host/minilua 2>/dev/null || true
+        mk="$(pick_make)"
+        "${mk}" -C "${local_dir}/src" host/minilua 2>/dev/null || true
         if [[ -x "${local_dir}/src/host/minilua" ]]; then
           "${local_dir}/src/host/minilua" "${local_dir}/src/genversion.lua" > "${local_dir}/src/luajit.h" 2>/dev/null || true
         fi
diff --git a/tools/stage_madng_headers_macos.sh b/tools/stage_madng_headers_macos.sh
index 16d051a..79a46e9 100755
--- a/tools/stage_madng_headers_macos.sh
+++ b/tools/stage_madng_headers_macos.sh
@@ -34,6 +34,14 @@ need_cmd() {
   command -v "$1" >/dev/null 2>&1 || { echo "Missing command: $1" >&2; exit 1; }
 }
 
+pick_make() {
+  if command -v gmake >/dev/null 2>&1; then
+    echo "gmake"
+  else
+    echo "make"
+  fi
+}
+
 fetch_tarball() {
   local url="$1"
   local out="$2"
@@ -109,12 +117,14 @@ main() {
     # Last resort: the MAD-patch fork generates luajit.h during build.
     if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
       echo "luajit.h not in repo — generating via make..."
+      mk="$(pick_make)"
       ( cd "${local_dir}/src"
-        make luajit.h 2>/dev/null || true
+        "${mk}" luajit.h 2>/dev/null || true
       )
       if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
         # macOS: try building minilua and running it manually if make target fails
-        make -C "${local_dir}/src" host/minilua 2>/dev/null || true
+        mk="$(pick_make)"
+        "${mk}" -C "${local_dir}/src" host/minilua 2>/dev/null || true
         if [[ -x "${local_dir}/src/host/minilua" ]]; then
           "${local_dir}/src/host/minilua" "${local_dir}/src/genversion.lua" > "${local_dir}/src/luajit.h" 2>/dev/null || true
         fi

From 85f32398b31af8887ba3e3367fee1be5b71d2dc7 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 23:29:41 +0200
Subject: [PATCH 22/69] Refactor Makefile to remove 'bg' commands and ensure
 valid indentation for sequential execution

---
 .github/workflows/compile_madng.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 1431d84..a2a5c6a 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -94,7 +94,9 @@ jobs:
 
         # Remove 'bg' commands from Makefile entirely (convert to sequential execution)
         # Preserve leading recipe indentation so Makefile separators remain valid.
-        sed -i.bak -E 's/^([[:space:]]*)bg[[:space:]]+([^[:space:]]+)[[:space:]]+([^[:space:]]+)$/\1\2 > \3/' Makefile
+        # Some Makefile lines have trailing tokens/comments; match and replace the
+        # leading `bg <script> <out>` portion only.
+        sed -i.bak -E 's/^([[:space:]]*)bg[[:space:]]+([^[:space:]]+)[[:space:]]+([^[:space:]]+).*/\1\2 > \3/' Makefile
 
         # Verify the sed worked by checking a few lines
         echo "=== Makefile after bg removal ==="

From d84b9daed5d29b51a06ef66a9c3846540f127aa7 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 23:33:45 +0200
Subject: [PATCH 23/69] Remove async "bg" helper from Makefile for CI
 compatibility and verify removal

---
 .github/workflows/compile_madng.yml | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index a2a5c6a..0a67bad 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -92,15 +92,22 @@ jobs:
           export LDFLAGS="-L$(brew --prefix libomp)/lib -lomp"
         fi
 
-        # Remove 'bg' commands from Makefile entirely (convert to sequential execution)
-        # Preserve leading recipe indentation so Makefile separators remain valid.
-        # Some Makefile lines have trailing tokens/comments; match and replace the
-        # leading `bg <script> <out>` portion only.
-        sed -i.bak -E 's/^([[:space:]]*)bg[[:space:]]+([^[:space:]]+)[[:space:]]+([^[:space:]]+).*/\1\2 > \3/' Makefile
+        # Remove MAD-NG's async "bg" helper from the Makefile for CI.
+        # It may appear either as the literal token `bg ...` or as `$(BG) ...`.
+        sed -i.bak -E \
+          -e 's/\$\((BG)\)[[:space:]]+([^[:space:]]+)[[:space:]]+([^[:space:]]+)/\2 > \3/g' \
+          -e 's/\$\{BG\}[[:space:]]+([^[:space:]]+)[[:space:]]+([^[:space:]]+)/\1 > \2/g' \
+          -e 's/^([[:space:]]*)bg[[:space:]]+([^[:space:]]+)[[:space:]]+([^[:space:]]+).*/\1\2 > \3/' \
+          Makefile
 
         # Verify the sed worked by checking a few lines
         echo "=== Makefile after bg removal ==="
-        grep -c "^[^#]*bg " Makefile && echo "WARNING: bg commands still present!" || echo "OK: bg commands removed"
+        if grep -nE '(^|[[:space:]])(bg|\$\((BG)\)|\$\{BG\})[[:space:]]+' Makefile; then
+          echo "WARNING: bg commands still present!"
+          exit 1
+        else
+          echo "OK: bg commands removed"
+        fi
 
         # Patch template syntax errors in mad_dynmap.cpp for GitHub Actions runner.
         # Adding 'typename' fixes C++ standard compliance without changing functionality.

From 4db441ca3e35e9f18d5104058d6d54dabadcc884 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 23:41:29 +0200
Subject: [PATCH 24/69] better luajit making

---
 tools/stage_madng_headers_linux.sh | 36 ++++++++---------------------
 tools/stage_madng_headers_macos.sh | 37 +++++++++---------------------
 2 files changed, 21 insertions(+), 52 deletions(-)

diff --git a/tools/stage_madng_headers_linux.sh b/tools/stage_madng_headers_linux.sh
index 3c5a405..a666cde 100755
--- a/tools/stage_madng_headers_linux.sh
+++ b/tools/stage_madng_headers_linux.sh
@@ -25,7 +25,7 @@ FFTW_VERSION="${FFTW_VERSION:-3.3.10}"
 NFFT_VERSION="${NFFT_VERSION:-3.5.3}"
 
 # Optional: point these at already-installed headers (will be copied/symlinked)
-LUAJIT_SRC_DIR="${LUAJIT_SRC_DIR:-}"   # directory containing lua.h etc
+LUAJIT_SRC_DIR="${LUAJIT_SRC_DIR:-}"   # directory containing lua.h, luajit.h, etc
 NLOPT_INC_DIR="${NLOPT_INC_DIR:-}"     # directory containing nlopt.h
 FFTW_INC_DIR="${FFTW_INC_DIR:-}"       # directory containing fftw3.h
 NFFT_INC_DIR="${NFFT_INC_DIR:-}"       # directory containing nfft3.h
@@ -86,6 +86,8 @@ main() {
   # LuaJIT headers -> lib/luajit/src/*
   if [[ -n "${LUAJIT_SRC_DIR}" ]]; then
     echo "Staging LuaJIT headers from LUAJIT_SRC_DIR=${LUAJIT_SRC_DIR}"
+    [[ -e "${LUAJIT_SRC_DIR}/lua.h" ]] || { echo "Missing ${LUAJIT_SRC_DIR}/lua.h" >&2; exit 1; }
+    [[ -e "${LUAJIT_SRC_DIR}/luajit.h" ]] || { echo "Missing ${LUAJIT_SRC_DIR}/luajit.h" >&2; exit 1; }
     mkdir -p "${LIB_DIR}/luajit"
     stage_dir_copy_or_link "${LUAJIT_SRC_DIR}" "${LIB_DIR}/luajit/src" "symlink"
   else
@@ -101,34 +103,16 @@ main() {
       git pull --ff-only || true
     )
 
-    # Some LuaJIT variants ship `luajit.h.in` instead of `luajit.h`.
-    if [[ ! -e "${local_dir}/src/luajit.h" && -e "${local_dir}/src/luajit.h.in" ]]; then
-      cp -f "${local_dir}/src/luajit.h.in" "${local_dir}/src/luajit.h"
-    fi
-
-    # Fallback: some forks may place the template elsewhere.
-    if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
-      alt="$(find "${local_dir}" -maxdepth 6 \( -name 'luajit.h.in' -o -name 'luajit.h' \) | head -n 1 || true)"
-      if [[ -n "${alt}" && -e "${alt}" ]]; then
-        cp -f "${alt}" "${local_dir}/src/luajit.h"
-      fi
-    fi
-
-    # Last resort: the MAD-patch fork generates luajit.h during build.
+    # Follow MAD's documented build flow for the mad-patch branch.
     if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
-      echo "luajit.h not in repo — generating via make..."
+      echo "luajit.h not in repo — building LuaJIT as documented by MAD..."
       mk="$(pick_make)"
-      ( cd "${local_dir}/src"
-        "${mk}" luajit.h 2>/dev/null || true
+      (
+        cd "${local_dir}"
+        "${mk}" clean
+        "${mk}" amalg PREFIX="$(pwd)"
+        "${mk}" install PREFIX="$(pwd)"
       )
-      if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
-        # Fallback: try building minilua and running it manually if make target fails
-        mk="$(pick_make)"
-        "${mk}" -C "${local_dir}/src" host/minilua 2>/dev/null || true
-        if [[ -x "${local_dir}/src/host/minilua" ]]; then
-          "${local_dir}/src/host/minilua" "${local_dir}/src/genversion.lua" > "${local_dir}/src/luajit.h" 2>/dev/null || true
-        fi
-      fi
     fi
   fi
 
diff --git a/tools/stage_madng_headers_macos.sh b/tools/stage_madng_headers_macos.sh
index 79a46e9..81f2549 100755
--- a/tools/stage_madng_headers_macos.sh
+++ b/tools/stage_madng_headers_macos.sh
@@ -25,7 +25,7 @@ FFTW_VERSION="${FFTW_VERSION:-3.3.10}"
 NFFT_VERSION="${NFFT_VERSION:-3.5.3}"
 
 # Optional: point these at already-installed headers (will be copied/symlinked)
-LUAJIT_SRC_DIR="${LUAJIT_SRC_DIR:-}"   # directory containing lua.h etc
+LUAJIT_SRC_DIR="${LUAJIT_SRC_DIR:-}"   # directory containing lua.h, luajit.h, etc
 NLOPT_INC_DIR="${NLOPT_INC_DIR:-}"     # directory containing nlopt.h
 FFTW_INC_DIR="${FFTW_INC_DIR:-}"       # directory containing fftw3.h
 NFFT_INC_DIR="${NFFT_INC_DIR:-}"       # directory containing nfft3.h
@@ -86,6 +86,8 @@ main() {
   # LuaJIT headers -> lib/luajit/src/*
   if [[ -n "${LUAJIT_SRC_DIR}" ]]; then
     echo "Staging LuaJIT headers from LUAJIT_SRC_DIR=${LUAJIT_SRC_DIR}"
+    [[ -e "${LUAJIT_SRC_DIR}/lua.h" ]] || { echo "Missing ${LUAJIT_SRC_DIR}/lua.h" >&2; exit 1; }
+    [[ -e "${LUAJIT_SRC_DIR}/luajit.h" ]] || { echo "Missing ${LUAJIT_SRC_DIR}/luajit.h" >&2; exit 1; }
     mkdir -p "${LIB_DIR}/luajit"
     stage_dir_copy_or_link "${LUAJIT_SRC_DIR}" "${LIB_DIR}/luajit/src" "symlink"
   else
@@ -101,34 +103,17 @@ main() {
       git pull --ff-only || true
     )
 
-    # Some LuaJIT variants ship `luajit.h.in` instead of `luajit.h`.
-    if [[ ! -e "${local_dir}/src/luajit.h" && -e "${local_dir}/src/luajit.h.in" ]]; then
-      cp -f "${local_dir}/src/luajit.h.in" "${local_dir}/src/luajit.h"
-    fi
-
-    # Fallback: some forks may place the template elsewhere.
-    if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
-      alt="$(find "${local_dir}" -maxdepth 3 \( -name 'luajit.h.in' -o -name 'luajit.h' \) | head -n 1 || true)"
-      if [[ -n "${alt}" && -e "${alt}" ]]; then
-        cp -f "${alt}" "${local_dir}/src/luajit.h"
-      fi
-    fi
-
-    # Last resort: the MAD-patch fork generates luajit.h during build.
+    # Follow MAD's documented build flow for the mad-patch branch.
     if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
-      echo "luajit.h not in repo — generating via make..."
+      echo "luajit.h not in repo — building LuaJIT as documented by MAD..."
       mk="$(pick_make)"
-      ( cd "${local_dir}/src"
-        "${mk}" luajit.h 2>/dev/null || true
+      (
+        cd "${local_dir}"
+        export MACOSX_DEPLOYMENT_TARGET="${MACOSX_DEPLOYMENT_TARGET:-11}"
+        "${mk}" clean
+        "${mk}" amalg PREFIX="$(pwd)"
+        "${mk}" install PREFIX="$(pwd)"
       )
-      if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
-        # macOS: try building minilua and running it manually if make target fails
-        mk="$(pick_make)"
-        "${mk}" -C "${local_dir}/src" host/minilua 2>/dev/null || true
-        if [[ -x "${local_dir}/src/host/minilua" ]]; then
-          "${local_dir}/src/host/minilua" "${local_dir}/src/genversion.lua" > "${local_dir}/src/luajit.h" 2>/dev/null || true
-        fi
-      fi
     fi
   fi
 

From fbe6d3eac7776dc1d24f59256d274ef205ab091d Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 23:46:23 +0200
Subject: [PATCH 25/69] Refactor compile_madng.yml to streamline compiler
 options and remove unused include paths

---
 .github/workflows/compile_madng.yml | 17 ++++++-----------
 1 file changed, 6 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 0a67bad..0b1de8e 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -75,21 +75,16 @@ jobs:
     - name: Compile MAD-NG
       working-directory: MAD/src
       run: |
-        # Absolute include paths.
-        LIB="$(cd ../lib && pwd)"
-        LIB_INCLUDES="-I${LIB}/luajit/src -I${LIB}/nlopt/src/api -I${LIB}/fftw3/api -I${LIB}/nfft3/include"
-
         if [ "$RUNNER_OS" = "Linux" ]; then
           export CC=gcc-11 CXX=g++-11
-          export CFLAGS="${CFLAGS:-} ${LIB_INCLUDES}"
-          export CXXFLAGS="${CXXFLAGS:-} -std=c++17 ${LIB_INCLUDES}"
         elif [ "$RUNNER_OS" = "macOS" ]; then
           llvm="$(brew --prefix llvm)"
+          libomp="$(brew --prefix libomp)"
           export PATH="${llvm}/bin:${PATH}"
           export CC="${llvm}/bin/clang" CXX="${llvm}/bin/clang++"
-          export CFLAGS="${CFLAGS:-} ${LIB_INCLUDES} -I$(brew --prefix libomp)/include"
-          export CXXFLAGS="${CXXFLAGS:-} -std=c++17 ${LIB_INCLUDES} -I$(brew --prefix libomp)/include"
-          export LDFLAGS="-L$(brew --prefix libomp)/lib -lomp"
+          export CCOPTIONS="-I${libomp}/include"
+          export CXXOPTIONS="-I${libomp}/include"
+          export LDOPTIONS="-L${libomp}/lib -lomp"
         fi
 
         # Remove MAD-NG's async "bg" helper from the Makefile for CI.
@@ -124,8 +119,8 @@ jobs:
 
         make SHELL=/bin/bash \
           CC="${CC}" CXX="${CXX}" \
-          CFLAGS="${CFLAGS:-}" CXXFLAGS="${CXXFLAGS:-}" \
-          LDFLAGS="${LDFLAGS:-}"
+          CCOPTIONS="${CCOPTIONS:-}" CXXOPTIONS="${CXXOPTIONS:-}" \
+          LDOPTIONS="${LDOPTIONS:-}"
 
     - name: Upload binary
       uses: actions/upload-artifact@v4

From 008e35a1f1d287c0f107fc933aba5f184469532e Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Wed, 13 May 2026 23:55:28 +0200
Subject: [PATCH 26/69] Update CI workflow to specify macOS version and set
 LDOPTIONS for compilation

---
 .github/workflows/compile_madng.yml | 20 ++------------------
 1 file changed, 2 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 0b1de8e..455aad8 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest]
+        os: [ubuntu-latest, macos-15-intel]
 
     steps:
     - name: Checkout current repo
@@ -77,6 +77,7 @@ jobs:
       run: |
         if [ "$RUNNER_OS" = "Linux" ]; then
           export CC=gcc-11 CXX=g++-11
+          export LDOPTIONS="-no-pie"
         elif [ "$RUNNER_OS" = "macOS" ]; then
           llvm="$(brew --prefix llvm)"
           libomp="$(brew --prefix libomp)"
@@ -87,23 +88,6 @@ jobs:
           export LDOPTIONS="-L${libomp}/lib -lomp"
         fi
 
-        # Remove MAD-NG's async "bg" helper from the Makefile for CI.
-        # It may appear either as the literal token `bg ...` or as `$(BG) ...`.
-        sed -i.bak -E \
-          -e 's/\$\((BG)\)[[:space:]]+([^[:space:]]+)[[:space:]]+([^[:space:]]+)/\2 > \3/g' \
-          -e 's/\$\{BG\}[[:space:]]+([^[:space:]]+)[[:space:]]+([^[:space:]]+)/\1 > \2/g' \
-          -e 's/^([[:space:]]*)bg[[:space:]]+([^[:space:]]+)[[:space:]]+([^[:space:]]+).*/\1\2 > \3/' \
-          Makefile
-
-        # Verify the sed worked by checking a few lines
-        echo "=== Makefile after bg removal ==="
-        if grep -nE '(^|[[:space:]])(bg|\$\((BG)\)|\$\{BG\})[[:space:]]+' Makefile; then
-          echo "WARNING: bg commands still present!"
-          exit 1
-        else
-          echo "OK: bg commands removed"
-        fi
-
         # Patch template syntax errors in mad_dynmap.cpp for GitHub Actions runner.
         # Adding 'typename' fixes C++ standard compliance without changing functionality.
         # Only patches the cloned copy in CI, not upstream.

From e8df36b189c87537de5199083c4357e7058d407f Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 00:05:58 +0200
Subject: [PATCH 27/69] Refactor CI workflow to separate Linux and macOS
 builds, streamline dependency installation, and update Makefile selection
 process

---
 .github/workflows/compile_madng.yml | 137 ++++++++++++++++------------
 1 file changed, 77 insertions(+), 60 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 455aad8..5207227 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -4,15 +4,13 @@ on:
   workflow_dispatch:
 
 jobs:
-  build:
-    runs-on: ${{ matrix.os }}
+  build-linux:
+    runs-on: ubuntu-22.04
+    container:
+      image: rockylinux:9
     defaults:
       run:
         shell: bash
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest, macos-15-intel]
 
     steps:
     - name: Checkout current repo
@@ -27,70 +25,32 @@ jobs:
 
     - name: Install dependencies
       run: |
-        if [ "$RUNNER_OS" = "Linux" ]; then
-          sudo apt-get update
-          sudo apt-get install -y build-essential gcc-11 g++-11
-        elif [ "$RUNNER_OS" = "macOS" ]; then
-          brew update
-          brew install llvm libomp make
-        fi
+        dnf install -y \
+          gcc gcc-c++ gcc-gfortran make git \
+          diffutils findutils sed which tar gzip
 
     - name: Select Makefile
       run: |
-        if [ "$RUNNER_OS" = "Linux" ]; then
-          cp MAD/src/Makefile.lxplus MAD/src/Makefile
-          sed -i \
-            -e 's#^CC[[:space:]]*=.*#CC=gcc-11#g' \
-            -e 's#^CXX[[:space:]]*=.*#CXX=g++-11#g' \
-            -e 's#-fdiagnostics-all-candidates##g' \
-            MAD/src/Makefile || true
-        elif [ "$RUNNER_OS" = "macOS" ]; then
-          brew_prefix_llvm="$(brew --prefix llvm)"
-          cp MAD/src/Makefile.macosx MAD/src/Makefile
-          sed -i.bak \
-            -e "s#^CC[[:space:]]*=[[:space:]]*gcc#CC=${brew_prefix_llvm}/bin/clang#g" \
-            -e "s#^CC[[:space:]]*=[[:space:]]*clang#CC=${brew_prefix_llvm}/bin/clang#g" \
-            -e "s#^CXX[[:space:]]*=[[:space:]]*g\\+\\+#CXX=${brew_prefix_llvm}/bin/clang++#g" \
-            -e "s#^CXX[[:space:]]*=[[:space:]]*clang\\+\\+#CXX=${brew_prefix_llvm}/bin/clang++#g" \
-            -e "s#-fdiagnostics-all-candidates##g" \
-            -e "s#-march=native##g" \
-            -e "s#-mtune=native##g" \
-            -e "s#-mfma##g" \
-            MAD/src/Makefile
-        fi
+        cp MAD/src/Makefile.lxplus MAD/src/Makefile
+        sed -i \
+          -e 's#^CC[[:space:]]*=.*#CC=gcc#g' \
+          -e 's#^CXX[[:space:]]*=.*#CXX=g++#g' \
+          -e 's#-fdiagnostics-all-candidates##g' \
+          MAD/src/Makefile || true
 
     - name: Stage MAD-NG headers
       run: |
         mkdir -p MAD/tools
-        if [ "$RUNNER_OS" = "Linux" ]; then
-          cp -f tools/stage_madng_headers_linux.sh MAD/tools/
-          chmod +x MAD/tools/stage_madng_headers_linux.sh
-          (cd MAD && ./tools/stage_madng_headers_linux.sh)
-        elif [ "$RUNNER_OS" = "macOS" ]; then
-          cp -f tools/stage_madng_headers_macos.sh MAD/tools/
-          chmod +x MAD/tools/stage_madng_headers_macos.sh
-          (cd MAD && ./tools/stage_madng_headers_macos.sh)
-        fi
+        cp -f tools/stage_madng_headers_linux.sh MAD/tools/
+        chmod +x MAD/tools/stage_madng_headers_linux.sh
+        (cd MAD && ./tools/stage_madng_headers_linux.sh)
 
     - name: Compile MAD-NG
       working-directory: MAD/src
       run: |
-        if [ "$RUNNER_OS" = "Linux" ]; then
-          export CC=gcc-11 CXX=g++-11
-          export LDOPTIONS="-no-pie"
-        elif [ "$RUNNER_OS" = "macOS" ]; then
-          llvm="$(brew --prefix llvm)"
-          libomp="$(brew --prefix libomp)"
-          export PATH="${llvm}/bin:${PATH}"
-          export CC="${llvm}/bin/clang" CXX="${llvm}/bin/clang++"
-          export CCOPTIONS="-I${libomp}/include"
-          export CXXOPTIONS="-I${libomp}/include"
-          export LDOPTIONS="-L${libomp}/lib -lomp"
-        fi
+        export CC=gcc CXX=g++
+        export LDOPTIONS="-no-pie"
 
-        # Patch template syntax errors in mad_dynmap.cpp for GitHub Actions runner.
-        # Adding 'typename' fixes C++ standard compliance without changing functionality.
-        # Only patches the cloned copy in CI, not upstream.
         if [ -f mad_dynmap.cpp ]; then
           sed -i.bak \
             -e 's/M::MT/typename M::MT/g' \
@@ -103,11 +63,68 @@ jobs:
 
         make SHELL=/bin/bash \
           CC="${CC}" CXX="${CXX}" \
-          CCOPTIONS="${CCOPTIONS:-}" CXXOPTIONS="${CXXOPTIONS:-}" \
           LDOPTIONS="${LDOPTIONS:-}"
 
     - name: Upload binary
       uses: actions/upload-artifact@v4
       with:
-        name: mad-${{ runner.os }}
+        name: mad-Linux
+        path: MAD/src/mad
+
+  build-macos:
+    runs-on: macos-15-intel
+    defaults:
+      run:
+        shell: bash
+
+    steps:
+    - name: Checkout current repo
+      uses: actions/checkout@v4
+
+    - name: Clone MAD-NG
+      uses: actions/checkout@v4
+      with:
+        repository: MethodicalAcceleratorDesign/MAD-NG
+        path: MAD
+        submodules: recursive
+
+    - name: Install dependencies
+      run: |
+        brew update
+        brew install gcc make
+
+    - name: Select Makefile
+      run: |
+        cp MAD/src/Makefile.macosx MAD/src/Makefile
+        sed -i.bak \
+          -e "s#-fdiagnostics-all-candidates##g" \
+          MAD/src/Makefile
+
+    - name: Stage MAD-NG headers
+      run: |
+        mkdir -p MAD/tools
+        cp -f tools/stage_madng_headers_macos.sh MAD/tools/
+        chmod +x MAD/tools/stage_madng_headers_macos.sh
+        (cd MAD && ./tools/stage_madng_headers_macos.sh)
+
+    - name: Compile MAD-NG
+      working-directory: MAD/src
+      run: |
+        gcc_prefix="$(brew --prefix gcc)"
+        gcc_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gcc-*' ! -name 'gcc-ar*' ! -name 'gcc-nm*' ! -name 'gcc-ranlib*' | sort | tail -n1)"
+        gxx_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'g++-*' | sort | tail -n1)"
+        gfortran_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gfortran-*' | sort | tail -n1)"
+        toolshim="${RUNNER_TEMP}/gcc-shim"
+        mkdir -p "${toolshim}"
+        ln -sf "${gcc_bin}" "${toolshim}/gcc"
+        ln -sf "${gxx_bin}" "${toolshim}/g++"
+        ln -sf "${gfortran_bin}" "${toolshim}/gfortran"
+        export PATH="${toolshim}:${PATH}"
+
+        make SHELL=/bin/bash
+
+    - name: Upload binary
+      uses: actions/upload-artifact@v4
+      with:
+        name: mad-macOS
         path: MAD/src/mad

From 7f130d102d7030e77020dae91017636d0cb55748 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 00:08:03 +0200
Subject: [PATCH 28/69] Refactor CI workflow for Linux build to use Docker,
 streamline dependency installation, and consolidate build steps

---
 .github/workflows/compile_madng.yml | 84 ++++++++++++++---------------
 1 file changed, 42 insertions(+), 42 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 5207227..254d8a8 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -6,8 +6,6 @@ on:
 jobs:
   build-linux:
     runs-on: ubuntu-22.04
-    container:
-      image: rockylinux:9
     defaults:
       run:
         shell: bash
@@ -23,47 +21,49 @@ jobs:
         path: MAD
         submodules: recursive
 
-    - name: Install dependencies
-      run: |
-        dnf install -y \
-          gcc gcc-c++ gcc-gfortran make git \
-          diffutils findutils sed which tar gzip
-
-    - name: Select Makefile
-      run: |
-        cp MAD/src/Makefile.lxplus MAD/src/Makefile
-        sed -i \
-          -e 's#^CC[[:space:]]*=.*#CC=gcc#g' \
-          -e 's#^CXX[[:space:]]*=.*#CXX=g++#g' \
-          -e 's#-fdiagnostics-all-candidates##g' \
-          MAD/src/Makefile || true
-
-    - name: Stage MAD-NG headers
-      run: |
-        mkdir -p MAD/tools
-        cp -f tools/stage_madng_headers_linux.sh MAD/tools/
-        chmod +x MAD/tools/stage_madng_headers_linux.sh
-        (cd MAD && ./tools/stage_madng_headers_linux.sh)
-
-    - name: Compile MAD-NG
-      working-directory: MAD/src
+    - name: Build MAD-NG in Rocky Linux 9
       run: |
-        export CC=gcc CXX=g++
-        export LDOPTIONS="-no-pie"
-
-        if [ -f mad_dynmap.cpp ]; then
-          sed -i.bak \
-            -e 's/M::MT/typename M::MT/g' \
-            -e 's/M::MP/typename M::MP/g' \
-            -e 's/M::T/typename M::T/g' \
-            -e 's/M::P/typename M::P/g' \
-            -e 's/M::R/typename M::R/g' \
-            mad_dynmap.cpp || true
-        fi
-
-        make SHELL=/bin/bash \
-          CC="${CC}" CXX="${CXX}" \
-          LDOPTIONS="${LDOPTIONS:-}"
+        docker run --rm \
+          -v "${GITHUB_WORKSPACE}:/work" \
+          -w /work \
+          rockylinux:9 \
+          bash -lc '
+            dnf install -y \
+              gcc gcc-c++ gcc-gfortran make git \
+              diffutils findutils sed which tar gzip
+
+            cp MAD/src/Makefile.lxplus MAD/src/Makefile
+            sed -i \
+              -e '"'"'s#^CC[[:space:]]*=.*#CC=gcc#g'"'"' \
+              -e '"'"'s#^CXX[[:space:]]*=.*#CXX=g++#g'"'"' \
+              -e '"'"'s#-fdiagnostics-all-candidates##g'"'"' \
+              MAD/src/Makefile || true
+
+            mkdir -p MAD/tools
+            cp -f tools/stage_madng_headers_linux.sh MAD/tools/
+            chmod +x MAD/tools/stage_madng_headers_linux.sh
+            (cd MAD && ./tools/stage_madng_headers_linux.sh)
+
+            cd MAD/src
+            export CC=gcc CXX=g++
+            export LDOPTIONS="-no-pie"
+
+            if [ -f mad_dynmap.cpp ]; then
+              sed -i.bak \
+                -e '"'"'s/M::MT/typename M::MT/g'"'"' \
+                -e '"'"'s/M::MP/typename M::MP/g'"'"' \
+                -e '"'"'s/M::T/typename M::T/g'"'"' \
+                -e '"'"'s/M::P/typename M::P/g'"'"' \
+                -e '"'"'s/M::R/typename M::R/g'"'"' \
+                mad_dynmap.cpp || true
+            fi
+
+            make SHELL=/bin/bash \
+              CC="${CC}" CXX="${CXX}" \
+              LDOPTIONS="${LDOPTIONS:-}"
+
+            chmod 755 mad
+          '
 
     - name: Upload binary
       uses: actions/upload-artifact@v4

From 040f35f122800a9230a4ab3ce4d061ea5846a83b Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 00:11:24 +0200
Subject: [PATCH 29/69] Add LuaJIT library handling in macOS build process

---
 .github/workflows/compile_madng.yml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 254d8a8..b7cb511 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -107,6 +107,14 @@ jobs:
         chmod +x MAD/tools/stage_madng_headers_macos.sh
         (cd MAD && ./tools/stage_madng_headers_macos.sh)
 
+        mkdir -p MAD/bin/macosx
+        if [ -f MAD/lib/luajit/src/libluajit.a ]; then
+          cp -f MAD/lib/luajit/src/libluajit.a MAD/bin/macosx/libluajit.a
+        else
+          echo "Missing MAD/lib/luajit/src/libluajit.a after LuaJIT staging" >&2
+          exit 1
+        fi
+
     - name: Compile MAD-NG
       working-directory: MAD/src
       run: |

From 2b20e6d99f0ff09df5b0bc7bb0ce2a321a5aa49e Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 00:37:55 +0200
Subject: [PATCH 30/69] Enhance build scripts for macOS and Linux: add static
 dependencies, streamline Makefile adjustments, and implement rebuilding of
 LuaFileSystem and LPeg against LuaJIT

---
 .github/workflows/compile_madng.yml | 23 +++++++-
 tools/stage_madng_headers_linux.sh  | 87 +++++++++++++++++++++++++++-
 tools/stage_madng_headers_macos.sh  | 90 ++++++++++++++++++++++++++++-
 3 files changed, 197 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index b7cb511..60f0982 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -30,6 +30,7 @@ jobs:
           bash -lc '
             dnf install -y \
               gcc gcc-c++ gcc-gfortran make git \
+              libstdc++-static libquadmath-devel \
               diffutils findutils sed which tar gzip
 
             cp MAD/src/Makefile.lxplus MAD/src/Makefile
@@ -91,13 +92,17 @@ jobs:
     - name: Install dependencies
       run: |
         brew update
-        brew install gcc make
+        brew install gcc make cmake automake libtool pkg-config
 
     - name: Select Makefile
       run: |
         cp MAD/src/Makefile.macosx MAD/src/Makefile
         sed -i.bak \
           -e "s#-fdiagnostics-all-candidates##g" \
+          -e "s#-flto##g" \
+          -e "s#-march=native##g" \
+          -e "s#-mtune=native##g" \
+          -e "s#-mfma##g" \
           MAD/src/Makefile
 
     - name: Stage MAD-NG headers
@@ -115,6 +120,22 @@ jobs:
           exit 1
         fi
 
+    - name: Rebuild macOS static dependencies
+      run: |
+        gcc_prefix="$(brew --prefix gcc)"
+        gcc_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gcc-*' ! -name 'gcc-ar*' ! -name 'gcc-nm*' ! -name 'gcc-ranlib*' | sort | tail -n1)"
+        gxx_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'g++-*' | sort | tail -n1)"
+        gfortran_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gfortran-*' | sort | tail -n1)"
+        toolshim="${RUNNER_TEMP}/gcc-shim"
+        mkdir -p "${toolshim}"
+        ln -sf "${gcc_bin}" "${toolshim}/gcc"
+        ln -sf "${gxx_bin}" "${toolshim}/g++"
+        ln -sf "${gfortran_bin}" "${toolshim}/gfortran"
+        PATH="${toolshim}:${PATH}" \
+          JOBS="$(sysctl -n hw.ncpu)" \
+          CC=gcc CXX=g++ FC=gfortran AR=ar RANLIB=ranlib \
+          ./tools/build_madng_deps_macos.sh
+
     - name: Compile MAD-NG
       working-directory: MAD/src
       run: |
diff --git a/tools/stage_madng_headers_linux.sh b/tools/stage_madng_headers_linux.sh
index a666cde..ddb3b3c 100755
--- a/tools/stage_madng_headers_linux.sh
+++ b/tools/stage_madng_headers_linux.sh
@@ -2,6 +2,7 @@
 set -euo pipefail
 
 # Stage headers into the layout expected by MAD-NG's unmodified `src/Makefile`.
+# The fetch/stage layout follows the documented MAD dependency build flow.
 #
 # Expected include paths (from `src/Makefile`):
 #   -I../lib/luajit/src            -> lua.h, luajit.h, luaconf.h, lualib.h, lauxlib.h, lua.hpp
@@ -14,9 +15,13 @@ set -euo pipefail
 
 ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
 LIB_DIR="${ROOT}/lib"
+BIN_DIR="${ROOT}/bin/linux"
 
 LUAJIT_REF="${LUAJIT_REF:-mad-patch}"
 LUAJIT_REPO="${LUAJIT_REPO:-https://github.com/MethodicalAcceleratorDesign/LuaJIT.git}"
+LFS_REF="${LFS_REF:-v1.8.0}"
+LFS_REPO="${LFS_REPO:-https://github.com/MethodicalAcceleratorDesign/luafilesystem.git}"
+LPEG_VERSION="${LPEG_VERSION:-1.1.0}"
 
 NLOPT_REF="${NLOPT_REF:-v2.7.1}"
 NLOPT_REPO="${NLOPT_REPO:-https://github.com/stevengj/nlopt.git}"
@@ -80,8 +85,79 @@ stage_file_copy_or_link() {
   esac
 }
 
+rebuild_lfs() {
+  echo "Rebuilding LuaFileSystem against rebuilt LuaJIT"
+  need_cmd git
+  local dir="${LIB_DIR}/lfs"
+  if [[ ! -d "${dir}/.git" ]]; then
+    git clone "${LFS_REPO}" "${dir}"
+  fi
+  (
+    cd "${dir}"
+    git fetch --all --tags
+    git checkout "${LFS_REF}" || git checkout -B "${LFS_REF}" "origin/${LFS_REF}"
+    git pull --ff-only || true
+    make clean || true
+    make lfs.a
+    mkdir -p "${BIN_DIR}"
+    cp -f liblfs.a "${BIN_DIR}/liblfs.a"
+  )
+}
+
+rebuild_lpeg() {
+  echo "Rebuilding LPeg against rebuilt LuaJIT"
+  need_cmd tar
+  local tar_name="lpeg-${LPEG_VERSION}.tar.gz"
+  local tar_path="${LIB_DIR}/${tar_name}"
+  local src_dir="${LIB_DIR}/lpeg-${LPEG_VERSION}"
+  local dir="${LIB_DIR}/lpeg"
+  local luajit_inc="${LIB_DIR}/luajit/include/luajit-2.1"
+  local luajit_lib="${LIB_DIR}/luajit/lib/libluajit-5.1.a"
+
+  if [[ ! -d "${src_dir}" ]]; then
+    fetch_tarball "http://www.inf.puc-rio.br/~roberto/lpeg/${tar_name}" "${tar_path}"
+    ( cd "${LIB_DIR}" && tar xzf "${tar_name}" )
+  fi
+  if [[ ! -e "${dir}" ]]; then
+    ln -s "lpeg-${LPEG_VERSION}" "${dir}"
+  fi
+
+  (
+    cd "${dir}"
+    cp -f makefile makefile.mad.bak
+    sed -i \
+      -e "s|^#\\?LUADIR\\s*=.*|LUADIR = ${luajit_inc}|" \
+      -e "s|^#\\?LUALIB\\s*=.*|LUALIB = ${luajit_lib}|" \
+      -e "s|^COPT\\s*=.*|COPT = -O3|" \
+      makefile
+    if ! grep -qE '^[[:space:]]*lpeg\.a:' makefile; then
+      awk '
+        BEGIN{done=0}
+        {print}
+        (!done && $0 ~ /^lpeg\.so:/){
+          print ""
+          print "lpeg.a: $(FILES)"
+          print "\tenv $(AR) -r lib$@ $(FILES)"
+          print ""
+          done=1
+        }
+      ' makefile > makefile.mad.tmp && mv makefile.mad.tmp makefile
+    fi
+    sed -i \
+      -e 's/^\(linux:\).*/\1 lpeg.a/' \
+      -e 's/^\(macosx:\).*/\1 lpeg.a/' \
+      -e 's/^clean:.*/& liblpeg.a/' \
+      makefile || true
+    make clean || true
+    make linux
+    mkdir -p "${BIN_DIR}"
+    cp -f liblpeg.a "${BIN_DIR}/liblpeg.a"
+  )
+}
+
 main() {
   mkdir -p "${LIB_DIR}"
+  local rebuilt_luajit=0
 
   # LuaJIT headers -> lib/luajit/src/*
   if [[ -n "${LUAJIT_SRC_DIR}" ]]; then
@@ -103,7 +179,10 @@ main() {
       git pull --ff-only || true
     )
 
-    # Follow MAD's documented build flow for the mad-patch branch.
+    # Follow `README.luajit` literally enough to materialize `src/luajit.h`:
+    #   make clean
+    #   make amalg PREFIX=`pwd`
+    #   make install PREFIX=`pwd`
     if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
       echo "luajit.h not in repo — building LuaJIT as documented by MAD..."
       mk="$(pick_make)"
@@ -113,9 +192,15 @@ main() {
         "${mk}" amalg PREFIX="$(pwd)"
         "${mk}" install PREFIX="$(pwd)"
       )
+      rebuilt_luajit=1
     fi
   fi
 
+  if [[ "${rebuilt_luajit}" -eq 1 ]]; then
+    rebuild_lfs
+    rebuild_lpeg
+  fi
+
   # NLOpt headers -> lib/nlopt/src/api/nlopt.h
   if [[ -n "${NLOPT_INC_DIR}" ]]; then
     echo "Staging NLOpt header from NLOPT_INC_DIR=${NLOPT_INC_DIR}"
diff --git a/tools/stage_madng_headers_macos.sh b/tools/stage_madng_headers_macos.sh
index 81f2549..eadd4aa 100755
--- a/tools/stage_madng_headers_macos.sh
+++ b/tools/stage_madng_headers_macos.sh
@@ -2,6 +2,7 @@
 set -euo pipefail
 
 # Stage headers into the layout expected by MAD-NG's unmodified `src/Makefile`.
+# The fetch/stage layout follows the documented MAD dependency build flow.
 #
 # Expected include paths (from `src/Makefile`):
 #   -I../lib/luajit/src            -> lua.h, luajit.h, etc
@@ -14,9 +15,13 @@ set -euo pipefail
 
 ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
 LIB_DIR="${ROOT}/lib"
+BIN_DIR="${ROOT}/bin/macosx"
 
 LUAJIT_REF="${LUAJIT_REF:-mad-patch}"
 LUAJIT_REPO="${LUAJIT_REPO:-https://github.com/MethodicalAcceleratorDesign/LuaJIT.git}"
+LFS_REF="${LFS_REF:-v1.8.0}"
+LFS_REPO="${LFS_REPO:-https://github.com/MethodicalAcceleratorDesign/luafilesystem.git}"
+LPEG_VERSION="${LPEG_VERSION:-1.1.0}"
 
 NLOPT_REF="${NLOPT_REF:-v2.7.1}"
 NLOPT_REPO="${NLOPT_REPO:-https://github.com/stevengj/nlopt.git}"
@@ -80,8 +85,81 @@ stage_file_copy_or_link() {
   esac
 }
 
+rebuild_lfs() {
+  echo "Rebuilding LuaFileSystem against rebuilt LuaJIT"
+  need_cmd git
+  local dir="${LIB_DIR}/lfs"
+  if [[ ! -d "${dir}/.git" ]]; then
+    git clone "${LFS_REPO}" "${dir}"
+  fi
+  (
+    export MACOSX_DEPLOYMENT_TARGET="${MACOSX_DEPLOYMENT_TARGET:-11}"
+    cd "${dir}"
+    git fetch --all --tags
+    git checkout "${LFS_REF}" || git checkout -B "${LFS_REF}" "origin/${LFS_REF}"
+    git pull --ff-only || true
+    make clean || true
+    make lfs.a
+    mkdir -p "${BIN_DIR}"
+    cp -f liblfs.a "${BIN_DIR}/liblfs.a"
+  )
+}
+
+rebuild_lpeg() {
+  echo "Rebuilding LPeg against rebuilt LuaJIT"
+  need_cmd tar
+  local tar_name="lpeg-${LPEG_VERSION}.tar.gz"
+  local tar_path="${LIB_DIR}/${tar_name}"
+  local src_dir="${LIB_DIR}/lpeg-${LPEG_VERSION}"
+  local dir="${LIB_DIR}/lpeg"
+  local luajit_inc="${LIB_DIR}/luajit/include/luajit-2.1"
+  local luajit_lib="${LIB_DIR}/luajit/lib/libluajit-5.1.a"
+
+  if [[ ! -d "${src_dir}" ]]; then
+    fetch_tarball "http://www.inf.puc-rio.br/~roberto/lpeg/${tar_name}" "${tar_path}"
+    ( cd "${LIB_DIR}" && tar xzf "${tar_name}" )
+  fi
+  if [[ ! -e "${dir}" ]]; then
+    ln -s "lpeg-${LPEG_VERSION}" "${dir}"
+  fi
+
+  (
+    export MACOSX_DEPLOYMENT_TARGET="${MACOSX_DEPLOYMENT_TARGET:-11}"
+    cd "${dir}"
+    cp -f makefile makefile.mad.bak
+    sed -i.bak \
+      -e "s|^#\\?LUADIR\\s*=.*|LUADIR = ${luajit_inc}|" \
+      -e "s|^#\\?LUALIB\\s*=.*|LUALIB = ${luajit_lib}|" \
+      -e "s|^COPT\\s*=.*|COPT = -O3|" \
+      makefile
+    if ! grep -qE '^[[:space:]]*lpeg\.a:' makefile; then
+      awk '
+        BEGIN{done=0}
+        {print}
+        (!done && $0 ~ /^lpeg\.so:/){
+          print ""
+          print "lpeg.a: $(FILES)"
+          print "\tenv $(AR) -r lib$@ $(FILES)"
+          print ""
+          done=1
+        }
+      ' makefile > makefile.mad.tmp && mv makefile.mad.tmp makefile
+    fi
+    sed -i.bak \
+      -e 's/^\(linux:\).*/\1 lpeg.a/' \
+      -e 's/^\(macosx:\).*/\1 lpeg.a/' \
+      -e 's/^clean:.*/& liblpeg.a/' \
+      makefile || true
+    make clean || true
+    make macosx
+    mkdir -p "${BIN_DIR}"
+    cp -f liblpeg.a "${BIN_DIR}/liblpeg.a"
+  )
+}
+
 main() {
   mkdir -p "${LIB_DIR}"
+  local rebuilt_luajit=0
 
   # LuaJIT headers -> lib/luajit/src/*
   if [[ -n "${LUAJIT_SRC_DIR}" ]]; then
@@ -103,7 +181,11 @@ main() {
       git pull --ff-only || true
     )
 
-    # Follow MAD's documented build flow for the mad-patch branch.
+    # Follow `README.luajit` literally enough to materialize `src/luajit.h`:
+    #   export MACOSX_DEPLOYMENT_TARGET=11
+    #   make clean
+    #   make amalg PREFIX=`pwd`
+    #   make install PREFIX=`pwd`
     if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
       echo "luajit.h not in repo — building LuaJIT as documented by MAD..."
       mk="$(pick_make)"
@@ -114,9 +196,15 @@ main() {
         "${mk}" amalg PREFIX="$(pwd)"
         "${mk}" install PREFIX="$(pwd)"
       )
+      rebuilt_luajit=1
     fi
   fi
 
+  if [[ "${rebuilt_luajit}" -eq 1 ]]; then
+    rebuild_lfs
+    rebuild_lpeg
+  fi
+
   # NLOpt headers -> lib/nlopt/src/api/nlopt.h
   if [[ -n "${NLOPT_INC_DIR}" ]]; then
     echo "Staging NLOpt header from NLOPT_INC_DIR=${NLOPT_INC_DIR}"

From 7140fb6672a390ee5f14f26308a45ac518a63747 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 00:41:42 +0200
Subject: [PATCH 31/69] Remove static dependency on libstdc++-static from Linux
 build process

---
 .github/workflows/compile_madng.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 60f0982..3264937 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -30,7 +30,7 @@ jobs:
           bash -lc '
             dnf install -y \
               gcc gcc-c++ gcc-gfortran make git \
-              libstdc++-static libquadmath-devel \
+              libquadmath-devel \
               diffutils findutils sed which tar gzip
 
             cp MAD/src/Makefile.lxplus MAD/src/Makefile

From bdbbc17810cb5213d3a7c63929e34851e71cb1ae Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 00:43:23 +0200
Subject: [PATCH 32/69] remove lfs ref

---
 tools/stage_madng_headers_linux.sh | 2 --
 tools/stage_madng_headers_macos.sh | 2 --
 2 files changed, 4 deletions(-)

diff --git a/tools/stage_madng_headers_linux.sh b/tools/stage_madng_headers_linux.sh
index ddb3b3c..c035e18 100755
--- a/tools/stage_madng_headers_linux.sh
+++ b/tools/stage_madng_headers_linux.sh
@@ -19,7 +19,6 @@ BIN_DIR="${ROOT}/bin/linux"
 
 LUAJIT_REF="${LUAJIT_REF:-mad-patch}"
 LUAJIT_REPO="${LUAJIT_REPO:-https://github.com/MethodicalAcceleratorDesign/LuaJIT.git}"
-LFS_REF="${LFS_REF:-v1.8.0}"
 LFS_REPO="${LFS_REPO:-https://github.com/MethodicalAcceleratorDesign/luafilesystem.git}"
 LPEG_VERSION="${LPEG_VERSION:-1.1.0}"
 
@@ -95,7 +94,6 @@ rebuild_lfs() {
   (
     cd "${dir}"
     git fetch --all --tags
-    git checkout "${LFS_REF}" || git checkout -B "${LFS_REF}" "origin/${LFS_REF}"
     git pull --ff-only || true
     make clean || true
     make lfs.a
diff --git a/tools/stage_madng_headers_macos.sh b/tools/stage_madng_headers_macos.sh
index eadd4aa..20779ca 100755
--- a/tools/stage_madng_headers_macos.sh
+++ b/tools/stage_madng_headers_macos.sh
@@ -19,7 +19,6 @@ BIN_DIR="${ROOT}/bin/macosx"
 
 LUAJIT_REF="${LUAJIT_REF:-mad-patch}"
 LUAJIT_REPO="${LUAJIT_REPO:-https://github.com/MethodicalAcceleratorDesign/LuaJIT.git}"
-LFS_REF="${LFS_REF:-v1.8.0}"
 LFS_REPO="${LFS_REPO:-https://github.com/MethodicalAcceleratorDesign/luafilesystem.git}"
 LPEG_VERSION="${LPEG_VERSION:-1.1.0}"
 
@@ -96,7 +95,6 @@ rebuild_lfs() {
     export MACOSX_DEPLOYMENT_TARGET="${MACOSX_DEPLOYMENT_TARGET:-11}"
     cd "${dir}"
     git fetch --all --tags
-    git checkout "${LFS_REF}" || git checkout -B "${LFS_REF}" "origin/${LFS_REF}"
     git pull --ff-only || true
     make clean || true
     make lfs.a

From f46f4568de0ac04bf276ca8d0e211836197af5db Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 00:48:46 +0200
Subject: [PATCH 33/69] more fixes

---
 tools/stage_madng_headers_linux.sh | 13 ++++++-------
 tools/stage_madng_headers_macos.sh | 13 ++++++-------
 2 files changed, 12 insertions(+), 14 deletions(-)

diff --git a/tools/stage_madng_headers_linux.sh b/tools/stage_madng_headers_linux.sh
index c035e18..3c6ff90 100755
--- a/tools/stage_madng_headers_linux.sh
+++ b/tools/stage_madng_headers_linux.sh
@@ -96,7 +96,7 @@ rebuild_lfs() {
     git fetch --all --tags
     git pull --ff-only || true
     make clean || true
-    make lfs.a
+    make AR=ar lfs.a
     mkdir -p "${BIN_DIR}"
     cp -f liblfs.a "${BIN_DIR}/liblfs.a"
   )
@@ -123,10 +123,10 @@ rebuild_lpeg() {
   (
     cd "${dir}"
     cp -f makefile makefile.mad.bak
-    sed -i \
-      -e "s|^#\\?LUADIR\\s*=.*|LUADIR = ${luajit_inc}|" \
-      -e "s|^#\\?LUALIB\\s*=.*|LUALIB = ${luajit_lib}|" \
-      -e "s|^COPT\\s*=.*|COPT = -O3|" \
+    sed -i -E \
+      -e "s|^[#[:space:]]*LUADIR[[:space:]]*=.*|LUADIR = ${luajit_inc}|" \
+      -e "s|^[#[:space:]]*LUALIB[[:space:]]*=.*|LUALIB = ${luajit_lib}|" \
+      -e "s|^COPT[[:space:]]*=.*|COPT = -O3|" \
       makefile
     if ! grep -qE '^[[:space:]]*lpeg\.a:' makefile; then
       awk '
@@ -144,10 +144,9 @@ rebuild_lpeg() {
     sed -i \
       -e 's/^\(linux:\).*/\1 lpeg.a/' \
       -e 's/^\(macosx:\).*/\1 lpeg.a/' \
-      -e 's/^clean:.*/& liblpeg.a/' \
       makefile || true
     make clean || true
-    make linux
+    make AR=ar linux
     mkdir -p "${BIN_DIR}"
     cp -f liblpeg.a "${BIN_DIR}/liblpeg.a"
   )
diff --git a/tools/stage_madng_headers_macos.sh b/tools/stage_madng_headers_macos.sh
index 20779ca..4677eea 100755
--- a/tools/stage_madng_headers_macos.sh
+++ b/tools/stage_madng_headers_macos.sh
@@ -97,7 +97,7 @@ rebuild_lfs() {
     git fetch --all --tags
     git pull --ff-only || true
     make clean || true
-    make lfs.a
+    make AR=ar lfs.a
     mkdir -p "${BIN_DIR}"
     cp -f liblfs.a "${BIN_DIR}/liblfs.a"
   )
@@ -125,10 +125,10 @@ rebuild_lpeg() {
     export MACOSX_DEPLOYMENT_TARGET="${MACOSX_DEPLOYMENT_TARGET:-11}"
     cd "${dir}"
     cp -f makefile makefile.mad.bak
-    sed -i.bak \
-      -e "s|^#\\?LUADIR\\s*=.*|LUADIR = ${luajit_inc}|" \
-      -e "s|^#\\?LUALIB\\s*=.*|LUALIB = ${luajit_lib}|" \
-      -e "s|^COPT\\s*=.*|COPT = -O3|" \
+    sed -i.bak -E \
+      -e "s|^[#[:space:]]*LUADIR[[:space:]]*=.*|LUADIR = ${luajit_inc}|" \
+      -e "s|^[#[:space:]]*LUALIB[[:space:]]*=.*|LUALIB = ${luajit_lib}|" \
+      -e "s|^COPT[[:space:]]*=.*|COPT = -O3|" \
       makefile
     if ! grep -qE '^[[:space:]]*lpeg\.a:' makefile; then
       awk '
@@ -146,10 +146,9 @@ rebuild_lpeg() {
     sed -i.bak \
       -e 's/^\(linux:\).*/\1 lpeg.a/' \
       -e 's/^\(macosx:\).*/\1 lpeg.a/' \
-      -e 's/^clean:.*/& liblpeg.a/' \
       makefile || true
     make clean || true
-    make macosx
+    make AR=ar macosx
     mkdir -p "${BIN_DIR}"
     cp -f liblpeg.a "${BIN_DIR}/liblpeg.a"
   )

From 06343d8f7c36b6769921734ff21b669165267b11 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 00:54:06 +0200
Subject: [PATCH 34/69] liblpeg fixes

---
 tools/stage_madng_headers_linux.sh | 32 +++++++++++++++++++-----------
 tools/stage_madng_headers_macos.sh | 32 +++++++++++++++++++-----------
 2 files changed, 40 insertions(+), 24 deletions(-)

diff --git a/tools/stage_madng_headers_linux.sh b/tools/stage_madng_headers_linux.sh
index 3c6ff90..8d41281 100755
--- a/tools/stage_madng_headers_linux.sh
+++ b/tools/stage_madng_headers_linux.sh
@@ -128,25 +128,21 @@ rebuild_lpeg() {
       -e "s|^[#[:space:]]*LUALIB[[:space:]]*=.*|LUALIB = ${luajit_lib}|" \
       -e "s|^COPT[[:space:]]*=.*|COPT = -O3|" \
       makefile
-    if ! grep -qE '^[[:space:]]*lpeg\.a:' makefile; then
+    if ! grep -qE '^[[:space:]]*liblpeg\.a:' makefile; then
       awk '
         BEGIN{done=0}
         {print}
         (!done && $0 ~ /^lpeg\.so:/){
           print ""
-          print "lpeg.a: $(FILES)"
-          print "\tenv $(AR) -r lib$@ $(FILES)"
+          print "liblpeg.a: $(FILES)"
+          print "\tenv $(AR) -r $@ $(FILES)"
           print ""
           done=1
         }
       ' makefile > makefile.mad.tmp && mv makefile.mad.tmp makefile
     fi
-    sed -i \
-      -e 's/^\(linux:\).*/\1 lpeg.a/' \
-      -e 's/^\(macosx:\).*/\1 lpeg.a/' \
-      makefile || true
     make clean || true
-    make AR=ar linux
+    make AR=ar LUADIR="${luajit_inc}" LUALIB="${luajit_lib}" liblpeg.a
     mkdir -p "${BIN_DIR}"
     cp -f liblpeg.a "${BIN_DIR}/liblpeg.a"
   )
@@ -228,8 +224,13 @@ main() {
     url="https://fftw.org/${tar_name}"
     fetch_tarball "${url}" "${tar_path}"
     ( cd "${LIB_DIR}" && tar xzf "${tar_name}" )
-    rm -f "${LIB_DIR}/fftw3"
-    ln -s "fftw-${FFTW_VERSION}" "${LIB_DIR}/fftw3"
+    rm -rf "${LIB_DIR}/fftw3"
+    mkdir -p "${LIB_DIR}/fftw3/api"
+    if [[ -e "${LIB_DIR}/fftw-${FFTW_VERSION}/api/fftw3.h" ]]; then
+      ln -s "${LIB_DIR}/fftw-${FFTW_VERSION}/api/fftw3.h" "${LIB_DIR}/fftw3/api/fftw3.h"
+    else
+      ln -s "${LIB_DIR}/fftw-${FFTW_VERSION}/fftw3.h" "${LIB_DIR}/fftw3/api/fftw3.h"
+    fi
   fi
 
   # NFFT headers -> lib/nfft3/include/nfft3.h
@@ -245,8 +246,15 @@ main() {
     url="https://www-user.tu-chemnitz.de/~potts/nfft/download/${tar_name}"
     fetch_tarball "${url}" "${tar_path}"
     ( cd "${LIB_DIR}" && tar xzf "${tar_name}" )
-    rm -f "${LIB_DIR}/nfft3"
-    ln -s "nfft-${NFFT_VERSION}" "${LIB_DIR}/nfft3"
+    rm -rf "${LIB_DIR}/nfft3"
+    mkdir -p "${LIB_DIR}/nfft3/include"
+    if [[ -d "${LIB_DIR}/nfft-${NFFT_VERSION}/include" ]]; then
+      for header in "${LIB_DIR}"/nfft-"${NFFT_VERSION}"/include/*; do
+        ln -s "${header}" "${LIB_DIR}/nfft3/include/$(basename "${header}")"
+      done
+    else
+      ln -s "${LIB_DIR}/nfft-${NFFT_VERSION}/nfft3.h" "${LIB_DIR}/nfft3/include/nfft3.h"
+    fi
   fi
 
   echo
diff --git a/tools/stage_madng_headers_macos.sh b/tools/stage_madng_headers_macos.sh
index 4677eea..ecf0160 100755
--- a/tools/stage_madng_headers_macos.sh
+++ b/tools/stage_madng_headers_macos.sh
@@ -130,25 +130,21 @@ rebuild_lpeg() {
       -e "s|^[#[:space:]]*LUALIB[[:space:]]*=.*|LUALIB = ${luajit_lib}|" \
       -e "s|^COPT[[:space:]]*=.*|COPT = -O3|" \
       makefile
-    if ! grep -qE '^[[:space:]]*lpeg\.a:' makefile; then
+    if ! grep -qE '^[[:space:]]*liblpeg\.a:' makefile; then
       awk '
         BEGIN{done=0}
         {print}
         (!done && $0 ~ /^lpeg\.so:/){
           print ""
-          print "lpeg.a: $(FILES)"
-          print "\tenv $(AR) -r lib$@ $(FILES)"
+          print "liblpeg.a: $(FILES)"
+          print "\tenv $(AR) -r $@ $(FILES)"
           print ""
           done=1
         }
       ' makefile > makefile.mad.tmp && mv makefile.mad.tmp makefile
     fi
-    sed -i.bak \
-      -e 's/^\(linux:\).*/\1 lpeg.a/' \
-      -e 's/^\(macosx:\).*/\1 lpeg.a/' \
-      makefile || true
     make clean || true
-    make AR=ar macosx
+    make AR=ar LUADIR="${luajit_inc}" LUALIB="${luajit_lib}" liblpeg.a
     mkdir -p "${BIN_DIR}"
     cp -f liblpeg.a "${BIN_DIR}/liblpeg.a"
   )
@@ -232,8 +228,13 @@ main() {
     url="https://fftw.org/${tar_name}"
     fetch_tarball "${url}" "${tar_path}"
     ( cd "${LIB_DIR}" && tar xzf "${tar_name}" )
-    rm -f "${LIB_DIR}/fftw3"
-    ln -s "fftw-${FFTW_VERSION}" "${LIB_DIR}/fftw3"
+    rm -rf "${LIB_DIR}/fftw3"
+    mkdir -p "${LIB_DIR}/fftw3/api"
+    if [[ -e "${LIB_DIR}/fftw-${FFTW_VERSION}/api/fftw3.h" ]]; then
+      ln -s "${LIB_DIR}/fftw-${FFTW_VERSION}/api/fftw3.h" "${LIB_DIR}/fftw3/api/fftw3.h"
+    else
+      ln -s "${LIB_DIR}/fftw-${FFTW_VERSION}/fftw3.h" "${LIB_DIR}/fftw3/api/fftw3.h"
+    fi
   fi
 
   # NFFT headers -> lib/nfft3/include/nfft3.h
@@ -249,8 +250,15 @@ main() {
     url="https://www-user.tu-chemnitz.de/~potts/nfft/download/${tar_name}"
     fetch_tarball "${url}" "${tar_path}"
     ( cd "${LIB_DIR}" && tar xzf "${tar_name}" )
-    rm -f "${LIB_DIR}/nfft3"
-    ln -s "nfft-${NFFT_VERSION}" "${LIB_DIR}/nfft3"
+    rm -rf "${LIB_DIR}/nfft3"
+    mkdir -p "${LIB_DIR}/nfft3/include"
+    if [[ -d "${LIB_DIR}/nfft-${NFFT_VERSION}/include" ]]; then
+      for header in "${LIB_DIR}"/nfft-"${NFFT_VERSION}"/include/*; do
+        ln -s "${header}" "${LIB_DIR}/nfft3/include/$(basename "${header}")"
+      done
+    else
+      ln -s "${LIB_DIR}/nfft-${NFFT_VERSION}/nfft3.h" "${LIB_DIR}/nfft3/include/nfft3.h"
+    fi
   fi
 
   echo

From 3ad30a9c4ab2b93d8085ea607b490a5e639997f5 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 01:04:04 +0200
Subject: [PATCH 35/69] Refactor build scripts for Linux and macOS: streamline
 dependency builds and remove legacy code

---
 .github/workflows/compile_madng.yml |  15 +-
 tools/README.deps.md                |  66 ++++++
 tools/build_madng_deps_linux.sh     | 321 ++++++++++++++++++++++++++++
 tools/build_madng_deps_macos.sh     | 316 +++++++++++++++++++++++++++
 tools/stage_madng_headers_linux.sh  |  75 -------
 tools/stage_madng_headers_macos.sh  |  77 -------
 6 files changed, 706 insertions(+), 164 deletions(-)
 create mode 100644 tools/README.deps.md
 create mode 100755 tools/build_madng_deps_linux.sh
 create mode 100755 tools/build_madng_deps_macos.sh

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 3264937..a2d3090 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -40,10 +40,9 @@ jobs:
               -e '"'"'s#-fdiagnostics-all-candidates##g'"'"' \
               MAD/src/Makefile || true
 
-            mkdir -p MAD/tools
-            cp -f tools/stage_madng_headers_linux.sh MAD/tools/
-            chmod +x MAD/tools/stage_madng_headers_linux.sh
-            (cd MAD && ./tools/stage_madng_headers_linux.sh)
+            cp -f tools/build_madng_deps_linux.sh MAD/tools/
+            chmod +x MAD/tools/build_madng_deps_linux.sh
+            (cd MAD && JOBS="$(nproc)" CC=gcc CXX=g++ FC=gfortran AR=ar RANLIB=ranlib ./tools/build_madng_deps_linux.sh)
 
             cd MAD/src
             export CC=gcc CXX=g++
@@ -112,14 +111,6 @@ jobs:
         chmod +x MAD/tools/stage_madng_headers_macos.sh
         (cd MAD && ./tools/stage_madng_headers_macos.sh)
 
-        mkdir -p MAD/bin/macosx
-        if [ -f MAD/lib/luajit/src/libluajit.a ]; then
-          cp -f MAD/lib/luajit/src/libluajit.a MAD/bin/macosx/libluajit.a
-        else
-          echo "Missing MAD/lib/luajit/src/libluajit.a after LuaJIT staging" >&2
-          exit 1
-        fi
-
     - name: Rebuild macOS static dependencies
       run: |
         gcc_prefix="$(brew --prefix gcc)"
diff --git a/tools/README.deps.md b/tools/README.deps.md
new file mode 100644
index 0000000..5275bae
--- /dev/null
+++ b/tools/README.deps.md
@@ -0,0 +1,66 @@
+# MAD-NG dependency build scripts
+
+These scripts download/build the third-party **static** libraries MAD-NG expects, and copy the resulting `*.a` files into the OS-specific `bin/` directory (matching the historical layout in `my_lib/`).
+
+## Linux
+
+```bash
+chmod +x tools/build_madng_deps_linux.sh
+./tools/build_madng_deps_linux.sh
+```
+
+Outputs into `bin/linux/`:
+
+- `libluajit.a`
+- `liblfs.a`
+- `liblpeg.a`
+- `liblapack.a`
+- `librefblas.a`
+- `libfftw3.a`
+- `libnfft3.a`
+- `libnlopt.a`
+
+## macOS
+
+Prereqs (typical Homebrew setup):
+
+```bash
+brew install cmake gcc make automake libtool pkg-config
+```
+
+Then:
+
+```bash
+chmod +x tools/build_madng_deps_macos.sh
+./tools/build_madng_deps_macos.sh
+```
+
+Outputs into `bin/macosx/` (same filenames as Linux).
+
+## “Fill in the necessary things”
+
+All knobs can be supplied as environment variables (no prompts), or left unset to be prompted:
+
+- Build tools: `JOBS`, `CC`, `CXX`, `FC`, `AR`, `RANLIB`
+- LuaJIT: `LUAJIT_REPO`, `LUAJIT_REF`
+- LuaFileSystem: `LFS_REPO`, `LFS_REF`
+- Versions/refs: `LPEG_VERSION`, `FFTW_VERSION`, `NFFT_VERSION`, `NLOPT_REF`, `LAPACK_REF`
+- macOS only: `MACOSX_DEPLOYMENT_TARGET`
+
+Example (Linux):
+
+```bash
+JOBS=16 CC=clang FC=gfortran LUAJIT_REF=mad-patch ./tools/build_madng_deps_linux.sh
+```
+
+## Header-only staging (no rebuild)
+
+If you already have `*.a` archives in `bin/linux` or `bin/macosx`, but your build
+fails on missing headers (e.g. `lua.h`, `fftw3.h`, `nlopt.h`), use:
+
+- `tools/stage_madng_headers_linux.sh`
+- `tools/stage_madng_headers_macos.sh`
+
+They populate `lib/luajit`, `lib/nlopt`, `lib/fftw3`, `lib/nfft3` with the
+expected header layout (by cloning/downloading sources, or by symlinking from
+your provided include directories).
diff --git a/tools/build_madng_deps_linux.sh b/tools/build_madng_deps_linux.sh
new file mode 100755
index 0000000..ed80d65
--- /dev/null
+++ b/tools/build_madng_deps_linux.sh
@@ -0,0 +1,321 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Builds MAD-NG third-party *static* libraries into: ./bin/linux
+#
+# This script is intentionally "fill-in friendly": override variables via env
+# or interactively when prompted.
+#
+# Example:
+#   ./tools/build_madng_deps_linux.sh
+#
+# Outputs (matching historical `my_lib`):
+#   bin/linux/libluajit.a
+#   bin/linux/liblfs.a
+#   bin/linux/liblpeg.a
+#   bin/linux/liblapack.a
+#   bin/linux/librefblas.a
+#   bin/linux/libfftw3.a
+#   bin/linux/libnfft3.a
+#   bin/linux/libnlopt.a
+
+ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+OS_TAG="linux"
+BIN_DIR="${ROOT}/bin/${OS_TAG}"
+LIB_DIR="${ROOT}/lib"
+
+JOBS="${JOBS:-}"
+CC="${CC:-}"
+CXX="${CXX:-}"
+FC="${FC:-}"
+AR="${AR:-}"
+RANLIB="${RANLIB:-}"
+
+LUAJIT_REF="${LUAJIT_REF:-mad-patch}"
+LUAJIT_REPO="${LUAJIT_REPO:-https://github.com/MethodicalAcceleratorDesign/LuaJIT.git}"
+
+LFS_REF="${LFS_REF:-}"
+LFS_REPO="${LFS_REPO:-https://github.com/MethodicalAcceleratorDesign/luafilesystem.git}"
+
+LPEG_VERSION="${LPEG_VERSION:-1.1.0}"
+FFTW_VERSION="${FFTW_VERSION:-3.3.10}"
+NFFT_VERSION="${NFFT_VERSION:-3.5.3}"
+NLOPT_REF="${NLOPT_REF:-v2.7.1}"
+LAPACK_REF="${LAPACK_REF:-v3.12.1}"
+
+prompt_default() {
+  local var_name="$1"
+  local prompt="$2"
+  local default="$3"
+  local current="${!var_name:-}"
+
+  if [[ -n "${current}" ]]; then
+    return 0
+  fi
+
+  local reply=""
+  read -r -p "${prompt} [${default}]: " reply || true
+  if [[ -z "${reply}" ]]; then
+    reply="${default}"
+  fi
+  printf -v "${var_name}" "%s" "${reply}"
+}
+
+need_cmd() {
+  command -v "$1" >/dev/null 2>&1 || {
+    echo "Missing required command: $1" >&2
+    exit 1
+  }
+}
+
+fetch_tarball() {
+  local url="$1"
+  local out="$2"
+  if [[ -f "${out}" ]]; then
+    return 0
+  fi
+  if command -v curl >/dev/null 2>&1; then
+    curl -L --fail "${url}" -o "${out}"
+  else
+    need_cmd wget
+    wget -O "${out}" "${url}"
+  fi
+}
+
+ensure_dirs() {
+  mkdir -p "${BIN_DIR}"
+  mkdir -p "${LIB_DIR}"
+}
+
+build_luajit() {
+  echo "== LuaJIT (${LUAJIT_REF}) =="
+  need_cmd git
+  need_cmd make
+
+  local dir="${LIB_DIR}/luajit"
+  if [[ ! -d "${dir}/.git" ]]; then
+    git clone "${LUAJIT_REPO}" "${dir}"
+  fi
+  ( cd "${dir}"
+    git fetch --all --tags
+    git checkout "${LUAJIT_REF}"
+    git pull --ff-only || true
+    make clean
+    make -j"${JOBS}" amalg PREFIX="$(pwd)"
+    make install PREFIX="$(pwd)"
+    cp -f src/libluajit.a "${BIN_DIR}/libluajit.a"
+  )
+}
+
+build_lfs() {
+  echo "== LuaFileSystem ${LFS_REF:+(${LFS_REF})} =="
+  need_cmd git
+  need_cmd make
+
+  local dir="${LIB_DIR}/lfs"
+  if [[ ! -d "${dir}/.git" ]]; then
+    git clone "${LFS_REPO}" "${dir}"
+  fi
+  ( cd "${dir}"
+    git fetch --all --tags
+    git pull --ff-only || true
+    if [[ -n "${LFS_REF}" ]]; then
+      git checkout "${LFS_REF}" || git checkout -B "${LFS_REF}" "origin/${LFS_REF}"
+    fi
+    make clean || true
+    make -j"${JOBS}" AR="${AR}" lfs.a
+    cp -f liblfs.a "${BIN_DIR}/liblfs.a"
+  )
+}
+
+build_lpeg() {
+  echo "== LPeg (${LPEG_VERSION}) =="
+  need_cmd make
+  need_cmd sed
+  need_cmd ar
+
+  local tar="lpeg-${LPEG_VERSION}.tar.gz"
+  local url="http://www.inf.puc-rio.br/~roberto/lpeg/${tar}"
+  local tar_path="${LIB_DIR}/${tar}"
+  local src_dir="${LIB_DIR}/lpeg-${LPEG_VERSION}"
+  local dir="${LIB_DIR}/lpeg"
+
+  if [[ ! -d "${src_dir}" ]]; then
+    fetch_tarball "${url}" "${tar_path}"
+    ( cd "${LIB_DIR}" && tar xzf "${tar}" )
+  fi
+  if [[ ! -e "${dir}" ]]; then
+    ln -s "lpeg-${LPEG_VERSION}" "${dir}"
+  fi
+
+  local luajit_inc="${LIB_DIR}/luajit/include/luajit-2.1"
+  local luajit_lib="${LIB_DIR}/luajit/lib/libluajit-5.1.a"
+  if [[ ! -f "${luajit_lib}" ]]; then
+    echo "LuaJIT static library not found at ${luajit_lib}" >&2
+    echo "Run LuaJIT step first (or adjust paths)." >&2
+    exit 1
+  fi
+
+  ( cd "${dir}"
+    if [[ ! -f makefile.mad.orig ]]; then
+      cp -f makefile makefile.mad.orig
+    else
+      cp -f makefile.mad.orig makefile
+    fi
+    sed -i -E \
+      -e "s|^[#[:space:]]*LUADIR[[:space:]]*=.*|LUADIR = ${luajit_inc}|" \
+      -e "s|^[#[:space:]]*LUALIB[[:space:]]*=.*|LUALIB = ${luajit_lib}|" \
+      -e "s|^[#[:space:]]*COPT[[:space:]]*=.*|COPT = -O3|" \
+      makefile
+    make clean || true
+    make -j"${JOBS}" CC="${CC}" LUADIR="${luajit_inc}" lpvm.o lpcap.o lptree.o lpcode.o lpprint.o lpcset.o
+    "${AR}" -r liblpeg.a lpvm.o lpcap.o lptree.o lpcode.o lpprint.o lpcset.o
+    "${RANLIB}" liblpeg.a
+    cp -f liblpeg.a "${BIN_DIR}/liblpeg.a"
+  )
+}
+
+build_lapack() {
+  echo "== LAPACK (${LAPACK_REF}) =="
+  need_cmd git
+  need_cmd make
+
+  local dir="${LIB_DIR}/lapack"
+  if [[ ! -d "${dir}/.git" ]]; then
+    git clone https://github.com/Reference-LAPACK/lapack "${dir}"
+  fi
+  ( cd "${dir}"
+    git fetch --all --tags
+    git checkout "${LAPACK_REF}"
+    cp -f make.inc.example make.inc
+    # Ensure PIC (LAPACK can be linked into shared objects, depending on MAD build)
+    sed -i \
+      -e 's/^\(CFLAGS[[:space:]]*=[[:space:]]*.*\)$/\1 -fPIC/' \
+      -e 's/^\(FFLAGS[[:space:]]*=[[:space:]]*.*\)$/\1 -fPIC/' \
+      -e 's/^\(FFLAGS_NOOPT[[:space:]]*=[[:space:]]*.*\)$/\1 -fPIC/' \
+      make.inc || true
+    make clean
+    make -j"${JOBS}" lib
+    cp -f liblapack.a "${BIN_DIR}/liblapack.a"
+    cp -f librefblas.a "${BIN_DIR}/librefblas.a"
+  )
+}
+
+build_fftw3() {
+  echo "== FFTW3 (${FFTW_VERSION}) =="
+  need_cmd make
+
+  local tar="fftw-${FFTW_VERSION}.tar.gz"
+  local url="https://fftw.org/${tar}"
+  local tar_path="${LIB_DIR}/${tar}"
+  local src_dir="${LIB_DIR}/fftw-${FFTW_VERSION}"
+  local dir="${LIB_DIR}/fftw3"
+
+  if [[ ! -d "${src_dir}" ]]; then
+    fetch_tarball "${url}" "${tar_path}"
+    ( cd "${LIB_DIR}" && tar xzf "${tar}" )
+  fi
+  if [[ ! -e "${dir}" ]]; then
+    ln -s "fftw-${FFTW_VERSION}" "${dir}"
+  fi
+
+  ( cd "${dir}"
+    ./configure --disable-shared CC="${CC}"
+    make clean || true
+    make -j"${JOBS}"
+    cp -f .libs/libfftw3.a "${BIN_DIR}/libfftw3.a"
+  )
+}
+
+build_nfft3() {
+  echo "== NFFT3 (${NFFT_VERSION}) =="
+  need_cmd make
+
+  local tar="nfft-${NFFT_VERSION}.tar.gz"
+  local url="http://www.nfft.org/download/${tar}"
+  local tar_path="${LIB_DIR}/${tar}"
+  local src_dir="${LIB_DIR}/nfft-${NFFT_VERSION}"
+  local dir="${LIB_DIR}/nfft3"
+
+  if [[ ! -d "${src_dir}" ]]; then
+    fetch_tarball "${url}" "${tar_path}"
+    ( cd "${LIB_DIR}" && tar xzf "${tar}" )
+  fi
+  if [[ ! -e "${dir}" ]]; then
+    ln -s "nfft-${NFFT_VERSION}" "${dir}"
+  fi
+
+  ( cd "${dir}"
+    ./configure --enable-all --disable-shared \
+      --with-fftw3="$(pwd)/../fftw3" \
+      --with-fftw3-libdir="$(pwd)/../fftw3/.libs" \
+      --with-fftw3-includedir="$(pwd)/../fftw3/api" \
+      CC="${CC}"
+    make clean || true
+    make -j"${JOBS}"
+    cp -f .libs/libnfft3.a "${BIN_DIR}/libnfft3.a"
+  )
+}
+
+build_nlopt() {
+  echo "== NLOpt (${NLOPT_REF}) =="
+  need_cmd git
+  need_cmd cmake
+  need_cmd make
+
+  local dir="${LIB_DIR}/nlopt"
+  if [[ ! -d "${dir}/.git" ]]; then
+    git clone https://github.com/stevengj/nlopt "${dir}"
+  fi
+
+  ( cd "${dir}"
+    git fetch --all --tags
+    git checkout "${NLOPT_REF}"
+    rm -rf build
+    mkdir -p build
+    cd build
+    cmake -DBUILD_SHARED_LIBS=OFF -DNLOPT_CXX=OFF -DCMAKE_C_COMPILER="${CC}" ..
+    make -j"${JOBS}"
+    cp -f libnlopt.a "${BIN_DIR}/libnlopt.a"
+  )
+}
+
+main() {
+  ensure_dirs
+
+  prompt_default JOBS "Parallel jobs (make -j)" "$(getconf _NPROCESSORS_ONLN 2>/dev/null || echo 4)"
+  prompt_default CC "C compiler (CC)" "gcc"
+  prompt_default CXX "C++ compiler (CXX)" "g++"
+  prompt_default FC "Fortran compiler (FC)" "gfortran"
+  prompt_default AR "Archiver (AR)" "ar"
+  prompt_default RANLIB "RANLIB" "ranlib"
+
+  need_cmd "${CC}"
+  need_cmd "${FC}"
+  need_cmd "${AR}"
+  need_cmd "${RANLIB}"
+  need_cmd tar
+
+  if ! command -v rg >/dev/null 2>&1; then
+    echo "Tip: install ripgrep ('rg') for better diagnostics; continuing without it."
+  fi
+
+  echo "Root: ${ROOT}"
+  echo "Lib sources: ${LIB_DIR}"
+  echo "Output: ${BIN_DIR}"
+  echo
+
+  build_luajit
+  build_lfs
+  build_lpeg
+  build_lapack
+  build_fftw3
+  build_nfft3
+  build_nlopt
+
+  echo
+  echo "Done. Built libraries in: ${BIN_DIR}"
+  ls -1 "${BIN_DIR}"
+}
+
+main "$@"
diff --git a/tools/build_madng_deps_macos.sh b/tools/build_madng_deps_macos.sh
new file mode 100755
index 0000000..9aa790a
--- /dev/null
+++ b/tools/build_madng_deps_macos.sh
@@ -0,0 +1,316 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Builds MAD-NG third-party *static* libraries into: ./bin/macosx
+#
+# You still need system build tools. Typical (Homebrew) prerequisites:
+#   brew install cmake gcc make automake libtool pkg-config
+#
+# Example:
+#   ./tools/build_madng_deps_macos.sh
+
+ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+OS_TAG="macosx"
+BIN_DIR="${ROOT}/bin/${OS_TAG}"
+LIB_DIR="${ROOT}/lib"
+
+JOBS="${JOBS:-}"
+CC="${CC:-}"
+CXX="${CXX:-}"
+FC="${FC:-}"
+AR="${AR:-}"
+RANLIB="${RANLIB:-}"
+
+MACOSX_DEPLOYMENT_TARGET="${MACOSX_DEPLOYMENT_TARGET:-11.0}"
+
+LUAJIT_REF="${LUAJIT_REF:-mad-patch}"
+LUAJIT_REPO="${LUAJIT_REPO:-https://github.com/MethodicalAcceleratorDesign/LuaJIT.git}"
+
+LFS_REF="${LFS_REF:-}"
+LFS_REPO="${LFS_REPO:-https://github.com/MethodicalAcceleratorDesign/luafilesystem.git}"
+
+LPEG_VERSION="${LPEG_VERSION:-1.1.0}"
+FFTW_VERSION="${FFTW_VERSION:-3.3.10}"
+NFFT_VERSION="${NFFT_VERSION:-3.5.3}"
+NLOPT_REF="${NLOPT_REF:-v2.7.1}"
+LAPACK_REF="${LAPACK_REF:-v3.12.1}"
+
+prompt_default() {
+  local var_name="$1"
+  local prompt="$2"
+  local default="$3"
+  local current="${!var_name:-}"
+  if [[ -n "${current}" ]]; then
+    return 0
+  fi
+  local reply=""
+  read -r -p "${prompt} [${default}]: " reply || true
+  if [[ -z "${reply}" ]]; then
+    reply="${default}"
+  fi
+  printf -v "${var_name}" "%s" "${reply}"
+}
+
+need_cmd() {
+  command -v "$1" >/dev/null 2>&1 || {
+    echo "Missing required command: $1" >&2
+    exit 1
+  }
+}
+
+sedi() {
+  # Portable in-place sed across GNU/BSD
+  if sed --version >/dev/null 2>&1; then
+    sed -i "$@"
+  else
+    sed -i '' "$@"
+  fi
+}
+
+fetch_tarball() {
+  local url="$1"
+  local out="$2"
+  if [[ -f "${out}" ]]; then
+    return 0
+  fi
+  if command -v curl >/dev/null 2>&1; then
+    curl -L --fail "${url}" -o "${out}"
+  else
+    need_cmd wget
+    wget -O "${out}" "${url}"
+  fi
+}
+
+ensure_dirs() {
+  mkdir -p "${BIN_DIR}"
+  mkdir -p "${LIB_DIR}"
+}
+
+build_luajit() {
+  echo "== LuaJIT (${LUAJIT_REF}) =="
+  need_cmd git
+  need_cmd make
+
+  local dir="${LIB_DIR}/luajit"
+  if [[ ! -d "${dir}/.git" ]]; then
+    git clone "${LUAJIT_REPO}" "${dir}"
+  fi
+  ( export MACOSX_DEPLOYMENT_TARGET
+    cd "${dir}"
+    git fetch --all --tags
+    git checkout "${LUAJIT_REF}"
+    git pull --ff-only || true
+    make clean
+    make -j"${JOBS}" amalg PREFIX="$(pwd)"
+    make install PREFIX="$(pwd)"
+    cp -f src/libluajit.a "${BIN_DIR}/libluajit.a"
+  )
+}
+
+build_lfs() {
+  echo "== LuaFileSystem ${LFS_REF:+(${LFS_REF})} =="
+  need_cmd git
+  need_cmd make
+
+  local dir="${LIB_DIR}/lfs"
+  if [[ ! -d "${dir}/.git" ]]; then
+    git clone "${LFS_REPO}" "${dir}"
+  fi
+  ( cd "${dir}"
+    git fetch --all --tags
+    git pull --ff-only || true
+    if [[ -n "${LFS_REF}" ]]; then
+      git checkout "${LFS_REF}" || git checkout -B "${LFS_REF}" "origin/${LFS_REF}"
+    fi
+    make clean || true
+    make -j"${JOBS}" AR="${AR}" lfs.a
+    cp -f liblfs.a "${BIN_DIR}/liblfs.a"
+  )
+}
+
+build_lpeg() {
+  echo "== LPeg (${LPEG_VERSION}) =="
+  need_cmd make
+  need_cmd ar
+
+  local tar="lpeg-${LPEG_VERSION}.tar.gz"
+  local url="http://www.inf.puc-rio.br/~roberto/lpeg/${tar}"
+  local tar_path="${LIB_DIR}/${tar}"
+  local src_dir="${LIB_DIR}/lpeg-${LPEG_VERSION}"
+  local dir="${LIB_DIR}/lpeg"
+
+  if [[ ! -d "${src_dir}" ]]; then
+    fetch_tarball "${url}" "${tar_path}"
+    ( cd "${LIB_DIR}" && tar xzf "${tar}" )
+  fi
+  if [[ ! -e "${dir}" ]]; then
+    ln -s "lpeg-${LPEG_VERSION}" "${dir}"
+  fi
+
+  local luajit_inc="${LIB_DIR}/luajit/include/luajit-2.1"
+  local luajit_lib="${LIB_DIR}/luajit/lib/libluajit-5.1.a"
+  if [[ ! -f "${luajit_lib}" ]]; then
+    echo "LuaJIT static library not found at ${luajit_lib}" >&2
+    echo "Run LuaJIT step first (or adjust paths)." >&2
+    exit 1
+  fi
+
+  ( cd "${dir}"
+    if [[ ! -f makefile.mad.orig ]]; then
+      cp -f makefile makefile.mad.orig
+    else
+      cp -f makefile.mad.orig makefile
+    fi
+    sedi \
+      -e "s|^[#[:space:]]*LUADIR[[:space:]]*=.*|LUADIR = ${luajit_inc}|" \
+      -e "s|^[#[:space:]]*LUALIB[[:space:]]*=.*|LUALIB = ${luajit_lib}|" \
+      -e "s|^[#[:space:]]*COPT[[:space:]]*=.*|COPT = -O3|" \
+      makefile
+    make clean || true
+    make -j"${JOBS}" CC="${CC}" LUADIR="${luajit_inc}" lpvm.o lpcap.o lptree.o lpcode.o lpprint.o lpcset.o
+    "${AR}" -r liblpeg.a lpvm.o lpcap.o lptree.o lpcode.o lpprint.o lpcset.o
+    "${RANLIB}" liblpeg.a
+    cp -f liblpeg.a "${BIN_DIR}/liblpeg.a"
+  )
+}
+
+build_lapack() {
+  echo "== LAPACK (${LAPACK_REF}) =="
+  need_cmd git
+  need_cmd make
+
+  local dir="${LIB_DIR}/lapack"
+  if [[ ! -d "${dir}/.git" ]]; then
+    git clone https://github.com/Reference-LAPACK/lapack "${dir}"
+  fi
+  ( cd "${dir}"
+    git fetch --all --tags
+    git checkout "${LAPACK_REF}"
+    cp -f make.inc.example make.inc
+    sedi \
+      -e 's/^\(CFLAGS[[:space:]]*=[[:space:]]*.*\)$/\1 -fPIC/' \
+      -e 's/^\(FFLAGS[[:space:]]*=[[:space:]]*.*\)$/\1 -fPIC/' \
+      -e 's/^\(FFLAGS_NOOPT[[:space:]]*=[[:space:]]*.*\)$/\1 -fPIC/' \
+      make.inc || true
+    make clean
+    make -j"${JOBS}" lib
+    cp -f liblapack.a "${BIN_DIR}/liblapack.a"
+    cp -f librefblas.a "${BIN_DIR}/librefblas.a"
+  )
+}
+
+build_fftw3() {
+  echo "== FFTW3 (${FFTW_VERSION}) =="
+  need_cmd make
+
+  local tar="fftw-${FFTW_VERSION}.tar.gz"
+  local url="https://fftw.org/${tar}"
+  local tar_path="${LIB_DIR}/${tar}"
+  local src_dir="${LIB_DIR}/fftw-${FFTW_VERSION}"
+  local dir="${LIB_DIR}/fftw3"
+
+  if [[ ! -d "${src_dir}" ]]; then
+    fetch_tarball "${url}" "${tar_path}"
+    ( cd "${LIB_DIR}" && tar xzf "${tar}" )
+  fi
+  if [[ ! -e "${dir}" ]]; then
+    ln -s "fftw-${FFTW_VERSION}" "${dir}"
+  fi
+
+  ( cd "${dir}"
+    ./configure --disable-shared CC="${CC}"
+    make clean || true
+    make -j"${JOBS}"
+    cp -f .libs/libfftw3.a "${BIN_DIR}/libfftw3.a"
+  )
+}
+
+build_nfft3() {
+  echo "== NFFT3 (${NFFT_VERSION}) =="
+  need_cmd make
+
+  local tar="nfft-${NFFT_VERSION}.tar.gz"
+  local url="http://www.nfft.org/download/${tar}"
+  local tar_path="${LIB_DIR}/${tar}"
+  local src_dir="${LIB_DIR}/nfft-${NFFT_VERSION}"
+  local dir="${LIB_DIR}/nfft3"
+
+  if [[ ! -d "${src_dir}" ]]; then
+    fetch_tarball "${url}" "${tar_path}"
+    ( cd "${LIB_DIR}" && tar xzf "${tar}" )
+  fi
+  if [[ ! -e "${dir}" ]]; then
+    ln -s "nfft-${NFFT_VERSION}" "${dir}"
+  fi
+
+  ( cd "${dir}"
+    ./configure --enable-all --disable-shared \
+      --with-fftw3="$(pwd)/../fftw3" \
+      --with-fftw3-libdir="$(pwd)/../fftw3/.libs" \
+      --with-fftw3-includedir="$(pwd)/../fftw3/api" \
+      CC="${CC}"
+    make clean || true
+    make -j"${JOBS}"
+    cp -f .libs/libnfft3.a "${BIN_DIR}/libnfft3.a"
+  )
+}
+
+build_nlopt() {
+  echo "== NLOpt (${NLOPT_REF}) =="
+  need_cmd git
+  need_cmd cmake
+  need_cmd make
+
+  local dir="${LIB_DIR}/nlopt"
+  if [[ ! -d "${dir}/.git" ]]; then
+    git clone https://github.com/stevengj/nlopt "${dir}"
+  fi
+
+  ( cd "${dir}"
+    git fetch --all --tags
+    git checkout "${NLOPT_REF}"
+    rm -rf build
+    mkdir -p build
+    cd build
+    cmake -DBUILD_SHARED_LIBS=OFF -DNLOPT_CXX=OFF -DCMAKE_C_COMPILER="${CC}" ..
+    make -j"${JOBS}"
+    cp -f libnlopt.a "${BIN_DIR}/libnlopt.a"
+  )
+}
+
+main() {
+  ensure_dirs
+
+  prompt_default JOBS "Parallel jobs (make -j)" "$(sysctl -n hw.ncpu 2>/dev/null || echo 4)"
+  prompt_default CC "C compiler (CC)" "clang"
+  prompt_default CXX "C++ compiler (CXX)" "clang++"
+  prompt_default FC "Fortran compiler (FC)" "gfortran"
+  prompt_default AR "Archiver (AR)" "ar"
+  prompt_default RANLIB "RANLIB" "ranlib"
+
+  need_cmd "${CC}"
+  need_cmd "${FC}"
+  need_cmd "${AR}"
+  need_cmd "${RANLIB}"
+  need_cmd tar
+
+  echo "Root: ${ROOT}"
+  echo "Lib sources: ${LIB_DIR}"
+  echo "Output: ${BIN_DIR}"
+  echo "MACOSX_DEPLOYMENT_TARGET: ${MACOSX_DEPLOYMENT_TARGET}"
+  echo
+
+  build_luajit
+  build_lfs
+  build_lpeg
+  build_lapack
+  build_fftw3
+  build_nfft3
+  build_nlopt
+
+  echo
+  echo "Done. Built libraries in: ${BIN_DIR}"
+  ls -1 "${BIN_DIR}"
+}
+
+main "$@"
diff --git a/tools/stage_madng_headers_linux.sh b/tools/stage_madng_headers_linux.sh
index 8d41281..e5c8f11 100755
--- a/tools/stage_madng_headers_linux.sh
+++ b/tools/stage_madng_headers_linux.sh
@@ -15,12 +15,8 @@ set -euo pipefail
 
 ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
 LIB_DIR="${ROOT}/lib"
-BIN_DIR="${ROOT}/bin/linux"
-
 LUAJIT_REF="${LUAJIT_REF:-mad-patch}"
 LUAJIT_REPO="${LUAJIT_REPO:-https://github.com/MethodicalAcceleratorDesign/LuaJIT.git}"
-LFS_REPO="${LFS_REPO:-https://github.com/MethodicalAcceleratorDesign/luafilesystem.git}"
-LPEG_VERSION="${LPEG_VERSION:-1.1.0}"
 
 NLOPT_REF="${NLOPT_REF:-v2.7.1}"
 NLOPT_REPO="${NLOPT_REPO:-https://github.com/stevengj/nlopt.git}"
@@ -84,73 +80,8 @@ stage_file_copy_or_link() {
   esac
 }
 
-rebuild_lfs() {
-  echo "Rebuilding LuaFileSystem against rebuilt LuaJIT"
-  need_cmd git
-  local dir="${LIB_DIR}/lfs"
-  if [[ ! -d "${dir}/.git" ]]; then
-    git clone "${LFS_REPO}" "${dir}"
-  fi
-  (
-    cd "${dir}"
-    git fetch --all --tags
-    git pull --ff-only || true
-    make clean || true
-    make AR=ar lfs.a
-    mkdir -p "${BIN_DIR}"
-    cp -f liblfs.a "${BIN_DIR}/liblfs.a"
-  )
-}
-
-rebuild_lpeg() {
-  echo "Rebuilding LPeg against rebuilt LuaJIT"
-  need_cmd tar
-  local tar_name="lpeg-${LPEG_VERSION}.tar.gz"
-  local tar_path="${LIB_DIR}/${tar_name}"
-  local src_dir="${LIB_DIR}/lpeg-${LPEG_VERSION}"
-  local dir="${LIB_DIR}/lpeg"
-  local luajit_inc="${LIB_DIR}/luajit/include/luajit-2.1"
-  local luajit_lib="${LIB_DIR}/luajit/lib/libluajit-5.1.a"
-
-  if [[ ! -d "${src_dir}" ]]; then
-    fetch_tarball "http://www.inf.puc-rio.br/~roberto/lpeg/${tar_name}" "${tar_path}"
-    ( cd "${LIB_DIR}" && tar xzf "${tar_name}" )
-  fi
-  if [[ ! -e "${dir}" ]]; then
-    ln -s "lpeg-${LPEG_VERSION}" "${dir}"
-  fi
-
-  (
-    cd "${dir}"
-    cp -f makefile makefile.mad.bak
-    sed -i -E \
-      -e "s|^[#[:space:]]*LUADIR[[:space:]]*=.*|LUADIR = ${luajit_inc}|" \
-      -e "s|^[#[:space:]]*LUALIB[[:space:]]*=.*|LUALIB = ${luajit_lib}|" \
-      -e "s|^COPT[[:space:]]*=.*|COPT = -O3|" \
-      makefile
-    if ! grep -qE '^[[:space:]]*liblpeg\.a:' makefile; then
-      awk '
-        BEGIN{done=0}
-        {print}
-        (!done && $0 ~ /^lpeg\.so:/){
-          print ""
-          print "liblpeg.a: $(FILES)"
-          print "\tenv $(AR) -r $@ $(FILES)"
-          print ""
-          done=1
-        }
-      ' makefile > makefile.mad.tmp && mv makefile.mad.tmp makefile
-    fi
-    make clean || true
-    make AR=ar LUADIR="${luajit_inc}" LUALIB="${luajit_lib}" liblpeg.a
-    mkdir -p "${BIN_DIR}"
-    cp -f liblpeg.a "${BIN_DIR}/liblpeg.a"
-  )
-}
-
 main() {
   mkdir -p "${LIB_DIR}"
-  local rebuilt_luajit=0
 
   # LuaJIT headers -> lib/luajit/src/*
   if [[ -n "${LUAJIT_SRC_DIR}" ]]; then
@@ -185,15 +116,9 @@ main() {
         "${mk}" amalg PREFIX="$(pwd)"
         "${mk}" install PREFIX="$(pwd)"
       )
-      rebuilt_luajit=1
     fi
   fi
 
-  if [[ "${rebuilt_luajit}" -eq 1 ]]; then
-    rebuild_lfs
-    rebuild_lpeg
-  fi
-
   # NLOpt headers -> lib/nlopt/src/api/nlopt.h
   if [[ -n "${NLOPT_INC_DIR}" ]]; then
     echo "Staging NLOpt header from NLOPT_INC_DIR=${NLOPT_INC_DIR}"
diff --git a/tools/stage_madng_headers_macos.sh b/tools/stage_madng_headers_macos.sh
index ecf0160..af1a62a 100755
--- a/tools/stage_madng_headers_macos.sh
+++ b/tools/stage_madng_headers_macos.sh
@@ -15,12 +15,8 @@ set -euo pipefail
 
 ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
 LIB_DIR="${ROOT}/lib"
-BIN_DIR="${ROOT}/bin/macosx"
-
 LUAJIT_REF="${LUAJIT_REF:-mad-patch}"
 LUAJIT_REPO="${LUAJIT_REPO:-https://github.com/MethodicalAcceleratorDesign/LuaJIT.git}"
-LFS_REPO="${LFS_REPO:-https://github.com/MethodicalAcceleratorDesign/luafilesystem.git}"
-LPEG_VERSION="${LPEG_VERSION:-1.1.0}"
 
 NLOPT_REF="${NLOPT_REF:-v2.7.1}"
 NLOPT_REPO="${NLOPT_REPO:-https://github.com/stevengj/nlopt.git}"
@@ -84,75 +80,8 @@ stage_file_copy_or_link() {
   esac
 }
 
-rebuild_lfs() {
-  echo "Rebuilding LuaFileSystem against rebuilt LuaJIT"
-  need_cmd git
-  local dir="${LIB_DIR}/lfs"
-  if [[ ! -d "${dir}/.git" ]]; then
-    git clone "${LFS_REPO}" "${dir}"
-  fi
-  (
-    export MACOSX_DEPLOYMENT_TARGET="${MACOSX_DEPLOYMENT_TARGET:-11}"
-    cd "${dir}"
-    git fetch --all --tags
-    git pull --ff-only || true
-    make clean || true
-    make AR=ar lfs.a
-    mkdir -p "${BIN_DIR}"
-    cp -f liblfs.a "${BIN_DIR}/liblfs.a"
-  )
-}
-
-rebuild_lpeg() {
-  echo "Rebuilding LPeg against rebuilt LuaJIT"
-  need_cmd tar
-  local tar_name="lpeg-${LPEG_VERSION}.tar.gz"
-  local tar_path="${LIB_DIR}/${tar_name}"
-  local src_dir="${LIB_DIR}/lpeg-${LPEG_VERSION}"
-  local dir="${LIB_DIR}/lpeg"
-  local luajit_inc="${LIB_DIR}/luajit/include/luajit-2.1"
-  local luajit_lib="${LIB_DIR}/luajit/lib/libluajit-5.1.a"
-
-  if [[ ! -d "${src_dir}" ]]; then
-    fetch_tarball "http://www.inf.puc-rio.br/~roberto/lpeg/${tar_name}" "${tar_path}"
-    ( cd "${LIB_DIR}" && tar xzf "${tar_name}" )
-  fi
-  if [[ ! -e "${dir}" ]]; then
-    ln -s "lpeg-${LPEG_VERSION}" "${dir}"
-  fi
-
-  (
-    export MACOSX_DEPLOYMENT_TARGET="${MACOSX_DEPLOYMENT_TARGET:-11}"
-    cd "${dir}"
-    cp -f makefile makefile.mad.bak
-    sed -i.bak -E \
-      -e "s|^[#[:space:]]*LUADIR[[:space:]]*=.*|LUADIR = ${luajit_inc}|" \
-      -e "s|^[#[:space:]]*LUALIB[[:space:]]*=.*|LUALIB = ${luajit_lib}|" \
-      -e "s|^COPT[[:space:]]*=.*|COPT = -O3|" \
-      makefile
-    if ! grep -qE '^[[:space:]]*liblpeg\.a:' makefile; then
-      awk '
-        BEGIN{done=0}
-        {print}
-        (!done && $0 ~ /^lpeg\.so:/){
-          print ""
-          print "liblpeg.a: $(FILES)"
-          print "\tenv $(AR) -r $@ $(FILES)"
-          print ""
-          done=1
-        }
-      ' makefile > makefile.mad.tmp && mv makefile.mad.tmp makefile
-    fi
-    make clean || true
-    make AR=ar LUADIR="${luajit_inc}" LUALIB="${luajit_lib}" liblpeg.a
-    mkdir -p "${BIN_DIR}"
-    cp -f liblpeg.a "${BIN_DIR}/liblpeg.a"
-  )
-}
-
 main() {
   mkdir -p "${LIB_DIR}"
-  local rebuilt_luajit=0
 
   # LuaJIT headers -> lib/luajit/src/*
   if [[ -n "${LUAJIT_SRC_DIR}" ]]; then
@@ -189,15 +118,9 @@ main() {
         "${mk}" amalg PREFIX="$(pwd)"
         "${mk}" install PREFIX="$(pwd)"
       )
-      rebuilt_luajit=1
     fi
   fi
 
-  if [[ "${rebuilt_luajit}" -eq 1 ]]; then
-    rebuild_lfs
-    rebuild_lpeg
-  fi
-
   # NLOpt headers -> lib/nlopt/src/api/nlopt.h
   if [[ -n "${NLOPT_INC_DIR}" ]]; then
     echo "Staging NLOpt header from NLOPT_INC_DIR=${NLOPT_INC_DIR}"

From e3d042ad67a85c0903ad3c300283e2382fefe0e7 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 01:08:24 +0200
Subject: [PATCH 36/69] copy tools correctly

---
 .github/workflows/compile_madng.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index a2d3090..74d880f 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -28,6 +28,8 @@ jobs:
           -w /work \
           rockylinux:9 \
           bash -lc '
+            set -euo pipefail
+
             dnf install -y \
               gcc gcc-c++ gcc-gfortran make git \
               libquadmath-devel \
@@ -40,6 +42,7 @@ jobs:
               -e '"'"'s#-fdiagnostics-all-candidates##g'"'"' \
               MAD/src/Makefile || true
 
+            mkdir -p MAD/tools
             cp -f tools/build_madng_deps_linux.sh MAD/tools/
             chmod +x MAD/tools/build_madng_deps_linux.sh
             (cd MAD && JOBS="$(nproc)" CC=gcc CXX=g++ FC=gfortran AR=ar RANLIB=ranlib ./tools/build_madng_deps_linux.sh)

From 021fc7b634c74683de733af9736303184eae378b Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 01:18:33 +0200
Subject: [PATCH 37/69] librefblas

---
 tools/build_madng_deps_linux.sh | 7 ++++---
 tools/build_madng_deps_macos.sh | 5 +++--
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/tools/build_madng_deps_linux.sh b/tools/build_madng_deps_linux.sh
index ed80d65..ecbb2f0 100755
--- a/tools/build_madng_deps_linux.sh
+++ b/tools/build_madng_deps_linux.sh
@@ -195,9 +195,10 @@ build_lapack() {
       -e 's/^\(FFLAGS_NOOPT[[:space:]]*=[[:space:]]*.*\)$/\1 -fPIC/' \
       make.inc || true
     make clean
-    make -j"${JOBS}" lib
-    cp -f liblapack.a "${BIN_DIR}/liblapack.a"
+    make -j"${JOBS}" blaslib
+    make -j"${JOBS}" lapacklib
     cp -f librefblas.a "${BIN_DIR}/librefblas.a"
+    cp -f liblapack.a "${BIN_DIR}/liblapack.a"
   )
 }
 
@@ -232,7 +233,7 @@ build_nfft3() {
   need_cmd make
 
   local tar="nfft-${NFFT_VERSION}.tar.gz"
-  local url="http://www.nfft.org/download/${tar}"
+  local url="https://www-user.tu-chemnitz.de/~potts/nfft/download/${tar}"
   local tar_path="${LIB_DIR}/${tar}"
   local src_dir="${LIB_DIR}/nfft-${NFFT_VERSION}"
   local dir="${LIB_DIR}/nfft3"
diff --git a/tools/build_madng_deps_macos.sh b/tools/build_madng_deps_macos.sh
index 9aa790a..159a2f4 100755
--- a/tools/build_madng_deps_macos.sh
+++ b/tools/build_madng_deps_macos.sh
@@ -193,9 +193,10 @@ build_lapack() {
       -e 's/^\(FFLAGS_NOOPT[[:space:]]*=[[:space:]]*.*\)$/\1 -fPIC/' \
       make.inc || true
     make clean
-    make -j"${JOBS}" lib
-    cp -f liblapack.a "${BIN_DIR}/liblapack.a"
+    make -j"${JOBS}" blaslib
+    make -j"${JOBS}" lapacklib
     cp -f librefblas.a "${BIN_DIR}/librefblas.a"
+    cp -f liblapack.a "${BIN_DIR}/liblapack.a"
   )
 }
 

From b6e9969d33e3592edbfda8ea7b42630e29fc93e2 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 01:31:32 +0200
Subject: [PATCH 38/69] more fixes

---
 .github/workflows/compile_madng.yml | 5 +++--
 tools/build_madng_deps_macos.sh     | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 74d880f..4f7c165 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -31,7 +31,7 @@ jobs:
             set -euo pipefail
 
             dnf install -y \
-              gcc gcc-c++ gcc-gfortran make git \
+              gcc gcc-c++ gcc-gfortran make cmake git \
               libquadmath-devel \
               diffutils findutils sed which tar gzip
 
@@ -125,7 +125,8 @@ jobs:
         ln -sf "${gcc_bin}" "${toolshim}/gcc"
         ln -sf "${gxx_bin}" "${toolshim}/g++"
         ln -sf "${gfortran_bin}" "${toolshim}/gfortran"
-        PATH="${toolshim}:${PATH}" \
+        brew_bin="$(brew --prefix)/bin"
+        PATH="${toolshim}:${brew_bin}:${PATH}" \
           JOBS="$(sysctl -n hw.ncpu)" \
           CC=gcc CXX=g++ FC=gfortran AR=ar RANLIB=ranlib \
           ./tools/build_madng_deps_macos.sh
diff --git a/tools/build_madng_deps_macos.sh b/tools/build_madng_deps_macos.sh
index 159a2f4..2cb0fe9 100755
--- a/tools/build_madng_deps_macos.sh
+++ b/tools/build_madng_deps_macos.sh
@@ -231,7 +231,7 @@ build_nfft3() {
   need_cmd make
 
   local tar="nfft-${NFFT_VERSION}.tar.gz"
-  local url="http://www.nfft.org/download/${tar}"
+  local url="https://www-user.tu-chemnitz.de/~potts/nfft/download/${tar}"
   local tar_path="${LIB_DIR}/${tar}"
   local src_dir="${LIB_DIR}/nfft-${NFFT_VERSION}"
   local dir="${LIB_DIR}/nfft3"

From 5ad7c2c70ff0997a1507d63100af285d1d81fa1a Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 01:44:54 +0200
Subject: [PATCH 39/69] linux lib gcc

---
 .github/workflows/compile_madng.yml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 4f7c165..39abd28 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -32,7 +32,7 @@ jobs:
 
             dnf install -y \
               gcc gcc-c++ gcc-gfortran make cmake git \
-              libquadmath-devel \
+              libquadmath-devel libstdc++-static \
               diffutils findutils sed which tar gzip
 
             cp MAD/src/Makefile.lxplus MAD/src/Makefile
@@ -49,7 +49,10 @@ jobs:
 
             cd MAD/src
             export CC=gcc CXX=g++
-            export LDOPTIONS="-no-pie"
+            # GCC keeps libgfortran.a/libquadmath.a in its private lib dir;
+            # add it so -Wl,-Bstatic can find them.
+            gcc_libdir="$(gcc -print-libgcc-file-name | xargs dirname)"
+            export LDOPTIONS="-no-pie -L${gcc_libdir}"
 
             if [ -f mad_dynmap.cpp ]; then
               sed -i.bak \

From 6988261c5a185785c6e8b5ec396893949f441027 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 01:46:08 +0200
Subject: [PATCH 40/69] remove replacments

---
 .github/workflows/compile_madng.yml | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 39abd28..8260d41 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -54,16 +54,6 @@ jobs:
             gcc_libdir="$(gcc -print-libgcc-file-name | xargs dirname)"
             export LDOPTIONS="-no-pie -L${gcc_libdir}"
 
-            if [ -f mad_dynmap.cpp ]; then
-              sed -i.bak \
-                -e '"'"'s/M::MT/typename M::MT/g'"'"' \
-                -e '"'"'s/M::MP/typename M::MP/g'"'"' \
-                -e '"'"'s/M::T/typename M::T/g'"'"' \
-                -e '"'"'s/M::P/typename M::P/g'"'"' \
-                -e '"'"'s/M::R/typename M::R/g'"'"' \
-                mad_dynmap.cpp || true
-            fi
-
             make SHELL=/bin/bash \
               CC="${CC}" CXX="${CXX}" \
               LDOPTIONS="${LDOPTIONS:-}"

From 0ae898ed37b02fd89702ab6bd8abfe89426e1b5f Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 01:51:51 +0200
Subject: [PATCH 41/69] add dnf plugins and enable crb for dependency
 installation; update build scripts to clean and configure nfft3

---
 .github/workflows/compile_madng.yml | 2 ++
 tools/build_madng_deps_linux.sh     | 6 ++++--
 tools/build_madng_deps_macos.sh     | 6 ++++--
 3 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 8260d41..d7704ca 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -30,6 +30,8 @@ jobs:
           bash -lc '
             set -euo pipefail
 
+            dnf install -y dnf-plugins-core
+            dnf config-manager --enable crb
             dnf install -y \
               gcc gcc-c++ gcc-gfortran make cmake git \
               libquadmath-devel libstdc++-static \
diff --git a/tools/build_madng_deps_linux.sh b/tools/build_madng_deps_linux.sh
index ecbb2f0..b8a6462 100755
--- a/tools/build_madng_deps_linux.sh
+++ b/tools/build_madng_deps_linux.sh
@@ -247,12 +247,14 @@ build_nfft3() {
   fi
 
   ( cd "${dir}"
-    ./configure --enable-all --disable-shared \
+    make distclean || true
+    ./configure --disable-shared \
       --with-fftw3="$(pwd)/../fftw3" \
       --with-fftw3-libdir="$(pwd)/../fftw3/.libs" \
       --with-fftw3-includedir="$(pwd)/../fftw3/api" \
       CC="${CC}"
-    make clean || true
+    # Only build the library — strip applications/examples/tests from SUBDIRS.
+    sed -i 's/^\(SUBDIRS[[:space:]]*=\).*/\1 include kernel/' Makefile
     make -j"${JOBS}"
     cp -f .libs/libnfft3.a "${BIN_DIR}/libnfft3.a"
   )
diff --git a/tools/build_madng_deps_macos.sh b/tools/build_madng_deps_macos.sh
index 2cb0fe9..bae35fd 100755
--- a/tools/build_madng_deps_macos.sh
+++ b/tools/build_madng_deps_macos.sh
@@ -245,12 +245,14 @@ build_nfft3() {
   fi
 
   ( cd "${dir}"
-    ./configure --enable-all --disable-shared \
+    make distclean || true
+    ./configure --disable-shared \
       --with-fftw3="$(pwd)/../fftw3" \
       --with-fftw3-libdir="$(pwd)/../fftw3/.libs" \
       --with-fftw3-includedir="$(pwd)/../fftw3/api" \
       CC="${CC}"
-    make clean || true
+    # Only build the library — strip applications/examples/tests from SUBDIRS.
+    sed -i.bak 's/^\(SUBDIRS[[:space:]]*=\).*/\1 include kernel/' Makefile
     make -j"${JOBS}"
     cp -f .libs/libnfft3.a "${BIN_DIR}/libnfft3.a"
   )

From 004fa3c887f700c1003ed8ece606e1dc85583a61 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 01:58:10 +0200
Subject: [PATCH 42/69] gfortran

---
 .github/workflows/compile_madng.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index d7704ca..b67968c 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -51,10 +51,11 @@ jobs:
 
             cd MAD/src
             export CC=gcc CXX=g++
-            # GCC keeps libgfortran.a/libquadmath.a in its private lib dir;
-            # add it so -Wl,-Bstatic can find them.
+            # LIBRARY_PATH makes GCC prepend -L at the START of the ld invocation,
+            # before -lgfortran/-lquadmath are seen (unlike LDOPTIONS which comes after).
             gcc_libdir="$(gcc -print-libgcc-file-name | xargs dirname)"
-            export LDOPTIONS="-no-pie -L${gcc_libdir}"
+            export LIBRARY_PATH="${gcc_libdir}${LIBRARY_PATH:+:${LIBRARY_PATH}}"
+            export LDOPTIONS="-no-pie"
 
             make SHELL=/bin/bash \
               CC="${CC}" CXX="${CXX}" \

From d0542daf0967b08190eccf2646c23b12fcf204be Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 02:05:22 +0200
Subject: [PATCH 43/69] static libs

---
 .github/workflows/compile_madng.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index b67968c..ee66c25 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -34,7 +34,8 @@ jobs:
             dnf config-manager --enable crb
             dnf install -y \
               gcc gcc-c++ gcc-gfortran make cmake git \
-              libquadmath-devel libstdc++-static \
+              libquadmath-devel libquadmath-static \
+              libgfortran-static libstdc++-static \
               diffutils findutils sed which tar gzip
 
             cp MAD/src/Makefile.lxplus MAD/src/Makefile

From ca0b0cf23345e9a5dba982c26d5291fdc56046eb Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 02:07:12 +0200
Subject: [PATCH 44/69] cmake

---
 tools/build_madng_deps_linux.sh | 3 ++-
 tools/build_madng_deps_macos.sh | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/tools/build_madng_deps_linux.sh b/tools/build_madng_deps_linux.sh
index b8a6462..d0596d7 100755
--- a/tools/build_madng_deps_linux.sh
+++ b/tools/build_madng_deps_linux.sh
@@ -277,7 +277,8 @@ build_nlopt() {
     rm -rf build
     mkdir -p build
     cd build
-    cmake -DBUILD_SHARED_LIBS=OFF -DNLOPT_CXX=OFF -DCMAKE_C_COMPILER="${CC}" ..
+    cmake -DBUILD_SHARED_LIBS=OFF -DNLOPT_CXX=OFF -DCMAKE_C_COMPILER="${CC}" \
+      -DCMAKE_POLICY_VERSION_MINIMUM=3.5 ..
     make -j"${JOBS}"
     cp -f libnlopt.a "${BIN_DIR}/libnlopt.a"
   )
diff --git a/tools/build_madng_deps_macos.sh b/tools/build_madng_deps_macos.sh
index bae35fd..4b8b97d 100755
--- a/tools/build_madng_deps_macos.sh
+++ b/tools/build_madng_deps_macos.sh
@@ -275,7 +275,8 @@ build_nlopt() {
     rm -rf build
     mkdir -p build
     cd build
-    cmake -DBUILD_SHARED_LIBS=OFF -DNLOPT_CXX=OFF -DCMAKE_C_COMPILER="${CC}" ..
+    cmake -DBUILD_SHARED_LIBS=OFF -DNLOPT_CXX=OFF -DCMAKE_C_COMPILER="${CC}" \
+      -DCMAKE_POLICY_VERSION_MINIMUM=3.5 ..
     make -j"${JOBS}"
     cp -f libnlopt.a "${BIN_DIR}/libnlopt.a"
   )

From 6f429c175d061250de7c7d98579ed99899a2820a Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 02:18:51 +0200
Subject: [PATCH 45/69] Bump NLOpt to v2.9.1 to fix CMake 4.x compatibility

v2.7.1 declares cmake_minimum_required(VERSION 2.x) which CMake 4.x
refuses to configure even with CMAKE_POLICY_VERSION_MINIMUM=3.5.
v2.9.1 requires CMake 3.15+ which is universally supported.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 tools/build_madng_deps_linux.sh | 2 +-
 tools/build_madng_deps_macos.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/build_madng_deps_linux.sh b/tools/build_madng_deps_linux.sh
index d0596d7..31c75c6 100755
--- a/tools/build_madng_deps_linux.sh
+++ b/tools/build_madng_deps_linux.sh
@@ -40,7 +40,7 @@ LFS_REPO="${LFS_REPO:-https://github.com/MethodicalAcceleratorDesign/luafilesyst
 LPEG_VERSION="${LPEG_VERSION:-1.1.0}"
 FFTW_VERSION="${FFTW_VERSION:-3.3.10}"
 NFFT_VERSION="${NFFT_VERSION:-3.5.3}"
-NLOPT_REF="${NLOPT_REF:-v2.7.1}"
+NLOPT_REF="${NLOPT_REF:-v2.9.1}"
 LAPACK_REF="${LAPACK_REF:-v3.12.1}"
 
 prompt_default() {
diff --git a/tools/build_madng_deps_macos.sh b/tools/build_madng_deps_macos.sh
index 4b8b97d..7a9f1ee 100755
--- a/tools/build_madng_deps_macos.sh
+++ b/tools/build_madng_deps_macos.sh
@@ -32,7 +32,7 @@ LFS_REPO="${LFS_REPO:-https://github.com/MethodicalAcceleratorDesign/luafilesyst
 LPEG_VERSION="${LPEG_VERSION:-1.1.0}"
 FFTW_VERSION="${FFTW_VERSION:-3.3.10}"
 NFFT_VERSION="${NFFT_VERSION:-3.5.3}"
-NLOPT_REF="${NLOPT_REF:-v2.7.1}"
+NLOPT_REF="${NLOPT_REF:-v2.9.1}"
 LAPACK_REF="${LAPACK_REF:-v3.12.1}"
 
 prompt_default() {

From 67c1d8028e545b3175b5bd476611dded44d88233 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 02:40:36 +0200
Subject: [PATCH 46/69] Reorder staging of MAD-NG headers in macOS build
 workflow

---
 .github/workflows/compile_madng.yml | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index ee66c25..da18e47 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -104,13 +104,6 @@ jobs:
           -e "s#-mfma##g" \
           MAD/src/Makefile
 
-    - name: Stage MAD-NG headers
-      run: |
-        mkdir -p MAD/tools
-        cp -f tools/stage_madng_headers_macos.sh MAD/tools/
-        chmod +x MAD/tools/stage_madng_headers_macos.sh
-        (cd MAD && ./tools/stage_madng_headers_macos.sh)
-
     - name: Rebuild macOS static dependencies
       run: |
         gcc_prefix="$(brew --prefix gcc)"
@@ -128,6 +121,13 @@ jobs:
           CC=gcc CXX=g++ FC=gfortran AR=ar RANLIB=ranlib \
           ./tools/build_madng_deps_macos.sh
 
+    - name: Stage MAD-NG headers
+      run: |
+        mkdir -p MAD/tools
+        cp -f tools/stage_madng_headers_macos.sh MAD/tools/
+        chmod +x MAD/tools/stage_madng_headers_macos.sh
+        (cd MAD && ./tools/stage_madng_headers_macos.sh)
+
     - name: Compile MAD-NG
       working-directory: MAD/src
       run: |

From 13853f38d34597ff3910bab6b7d6b6ee3d5f2656 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 12:59:49 +0200
Subject: [PATCH 47/69] add arm compilation

---
 .github/workflows/compile_madng.yml | 79 +++++++++++++++++++++++++++++
 1 file changed, 79 insertions(+)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index da18e47..68d9506 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -149,3 +149,82 @@ jobs:
       with:
         name: mad-macOS
         path: MAD/src/mad
+
+  build-macos-arm:
+    runs-on: macos-15-arm64
+    defaults:
+      run:
+        shell: bash
+
+    steps:
+    - name: Checkout current repo
+      uses: actions/checkout@v4
+
+    - name: Clone MAD-NG
+      uses: actions/checkout@v4
+      with:
+        repository: MethodicalAcceleratorDesign/MAD-NG
+        path: MAD
+        submodules: recursive
+
+    - name: Install dependencies
+      run: |
+        brew update
+        brew install gcc make cmake automake libtool pkg-config
+
+    - name: Select Makefile
+      run: |
+        cp MAD/src/Makefile.macosx MAD/src/Makefile
+        sed -i.bak \
+          -e "s#-fdiagnostics-all-candidates##g" \
+          -e "s#-flto##g" \
+          -e "s#-march=native##g" \
+          -e "s#-mtune=native##g" \
+          -e "s#-mfma##g" \
+          MAD/src/Makefile
+
+    - name: Rebuild macOS ARM static dependencies
+      run: |
+        gcc_prefix="$(brew --prefix gcc)"
+        gcc_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gcc-*' ! -name 'gcc-ar*' ! -name 'gcc-nm*' ! -name 'gcc-ranlib*' | sort | tail -n1)"
+        gxx_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'g++-*' | sort | tail -n1)"
+        gfortran_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gfortran-*' | sort | tail -n1)"
+        toolshim="${RUNNER_TEMP}/gcc-shim"
+        mkdir -p "${toolshim}"
+        ln -sf "${gcc_bin}" "${toolshim}/gcc"
+        ln -sf "${gxx_bin}" "${toolshim}/g++"
+        ln -sf "${gfortran_bin}" "${toolshim}/gfortran"
+        brew_bin="$(brew --prefix)/bin"
+        PATH="${toolshim}:${brew_bin}:${PATH}" \
+          JOBS="$(sysctl -n hw.ncpu)" \
+          CC=gcc CXX=g++ FC=gfortran AR=ar RANLIB=ranlib \
+          ./tools/build_madng_deps_macos.sh
+
+    - name: Stage MAD-NG headers
+      run: |
+        mkdir -p MAD/tools
+        cp -f tools/stage_madng_headers_macos.sh MAD/tools/
+        chmod +x MAD/tools/stage_madng_headers_macos.sh
+        (cd MAD && ./tools/stage_madng_headers_macos.sh)
+
+    - name: Compile MAD-NG
+      working-directory: MAD/src
+      run: |
+        gcc_prefix="$(brew --prefix gcc)"
+        gcc_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gcc-*' ! -name 'gcc-ar*' ! -name 'gcc-nm*' ! -name 'gcc-ranlib*' | sort | tail -n1)"
+        gxx_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'g++-*' | sort | tail -n1)"
+        gfortran_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gfortran-*' | sort | tail -n1)"
+        toolshim="${RUNNER_TEMP}/gcc-shim"
+        mkdir -p "${toolshim}"
+        ln -sf "${gcc_bin}" "${toolshim}/gcc"
+        ln -sf "${gxx_bin}" "${toolshim}/g++"
+        ln -sf "${gfortran_bin}" "${toolshim}/gfortran"
+        export PATH="${toolshim}:${PATH}"
+
+        make SHELL=/bin/bash
+
+    - name: Upload binary
+      uses: actions/upload-artifact@v4
+      with:
+        name: mad-macOS-ARM
+        path: MAD/src/mad

From 7d00c1e6ba342faaa2daeca881932d531ed08e64 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 13:02:48 +0200
Subject: [PATCH 48/69] actual name

---
 .github/workflows/compile_madng.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 68d9506..fde7c56 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -151,7 +151,7 @@ jobs:
         path: MAD/src/mad
 
   build-macos-arm:
-    runs-on: macos-15-arm64
+    runs-on: macos-latest
     defaults:
       run:
         shell: bash

From fd9f7fccafc06763662b7d8e5363992224c45f41 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 13:22:07 +0200
Subject: [PATCH 49/69] Refactor macOS ARM build workflow: remove legacy steps
 and enhance Makefile configuration

---
 .github/workflows/compile_madng.yml | 90 +++--------------------------
 1 file changed, 9 insertions(+), 81 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index fde7c56..8b60b37 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -71,85 +71,6 @@ jobs:
         name: mad-Linux
         path: MAD/src/mad
 
-  build-macos:
-    runs-on: macos-15-intel
-    defaults:
-      run:
-        shell: bash
-
-    steps:
-    - name: Checkout current repo
-      uses: actions/checkout@v4
-
-    - name: Clone MAD-NG
-      uses: actions/checkout@v4
-      with:
-        repository: MethodicalAcceleratorDesign/MAD-NG
-        path: MAD
-        submodules: recursive
-
-    - name: Install dependencies
-      run: |
-        brew update
-        brew install gcc make cmake automake libtool pkg-config
-
-    - name: Select Makefile
-      run: |
-        cp MAD/src/Makefile.macosx MAD/src/Makefile
-        sed -i.bak \
-          -e "s#-fdiagnostics-all-candidates##g" \
-          -e "s#-flto##g" \
-          -e "s#-march=native##g" \
-          -e "s#-mtune=native##g" \
-          -e "s#-mfma##g" \
-          MAD/src/Makefile
-
-    - name: Rebuild macOS static dependencies
-      run: |
-        gcc_prefix="$(brew --prefix gcc)"
-        gcc_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gcc-*' ! -name 'gcc-ar*' ! -name 'gcc-nm*' ! -name 'gcc-ranlib*' | sort | tail -n1)"
-        gxx_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'g++-*' | sort | tail -n1)"
-        gfortran_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gfortran-*' | sort | tail -n1)"
-        toolshim="${RUNNER_TEMP}/gcc-shim"
-        mkdir -p "${toolshim}"
-        ln -sf "${gcc_bin}" "${toolshim}/gcc"
-        ln -sf "${gxx_bin}" "${toolshim}/g++"
-        ln -sf "${gfortran_bin}" "${toolshim}/gfortran"
-        brew_bin="$(brew --prefix)/bin"
-        PATH="${toolshim}:${brew_bin}:${PATH}" \
-          JOBS="$(sysctl -n hw.ncpu)" \
-          CC=gcc CXX=g++ FC=gfortran AR=ar RANLIB=ranlib \
-          ./tools/build_madng_deps_macos.sh
-
-    - name: Stage MAD-NG headers
-      run: |
-        mkdir -p MAD/tools
-        cp -f tools/stage_madng_headers_macos.sh MAD/tools/
-        chmod +x MAD/tools/stage_madng_headers_macos.sh
-        (cd MAD && ./tools/stage_madng_headers_macos.sh)
-
-    - name: Compile MAD-NG
-      working-directory: MAD/src
-      run: |
-        gcc_prefix="$(brew --prefix gcc)"
-        gcc_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gcc-*' ! -name 'gcc-ar*' ! -name 'gcc-nm*' ! -name 'gcc-ranlib*' | sort | tail -n1)"
-        gxx_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'g++-*' | sort | tail -n1)"
-        gfortran_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gfortran-*' | sort | tail -n1)"
-        toolshim="${RUNNER_TEMP}/gcc-shim"
-        mkdir -p "${toolshim}"
-        ln -sf "${gcc_bin}" "${toolshim}/gcc"
-        ln -sf "${gxx_bin}" "${toolshim}/g++"
-        ln -sf "${gfortran_bin}" "${toolshim}/gfortran"
-        export PATH="${toolshim}:${PATH}"
-
-        make SHELL=/bin/bash
-
-    - name: Upload binary
-      uses: actions/upload-artifact@v4
-      with:
-        name: mad-macOS
-        path: MAD/src/mad
-
   build-macos-arm:
     runs-on: macos-latest
     defaults:
@@ -176,6 +97,9 @@ jobs:
       run: |
         cp MAD/src/Makefile.macosx MAD/src/Makefile
         sed -i.bak \
+          -e "s#^CC[[:space:]]*:=.*#CC       := gcc#g" \
+          -e "s#^CXX[[:space:]]*:=.*#CXX      := g++#g" \
+          -e "s#^FC[[:space:]]*:=.*#FC       := gfortran#g" \
           -e "s#-fdiagnostics-all-candidates##g" \
           -e "s#-flto##g" \
           -e "s#-march=native##g" \
@@ -189,6 +113,7 @@ jobs:
         gcc_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gcc-*' ! -name 'gcc-ar*' ! -name 'gcc-nm*' ! -name 'gcc-ranlib*' | sort | tail -n1)"
         gxx_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'g++-*' | sort | tail -n1)"
         gfortran_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gfortran-*' | sort | tail -n1)"
+        test -n "${gcc_bin}" && test -n "${gxx_bin}" && test -n "${gfortran_bin}"
         toolshim="${RUNNER_TEMP}/gcc-shim"
         mkdir -p "${toolshim}"
         ln -sf "${gcc_bin}" "${toolshim}/gcc"
@@ -214,14 +139,17 @@ jobs:
         gcc_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gcc-*' ! -name 'gcc-ar*' ! -name 'gcc-nm*' ! -name 'gcc-ranlib*' | sort | tail -n1)"
         gxx_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'g++-*' | sort | tail -n1)"
         gfortran_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gfortran-*' | sort | tail -n1)"
+        test -n "${gcc_bin}" && test -n "${gxx_bin}" && test -n "${gfortran_bin}"
         toolshim="${RUNNER_TEMP}/gcc-shim"
         mkdir -p "${toolshim}"
         ln -sf "${gcc_bin}" "${toolshim}/gcc"
         ln -sf "${gxx_bin}" "${toolshim}/g++"
         ln -sf "${gfortran_bin}" "${toolshim}/gfortran"
-        export PATH="${toolshim}:${PATH}"
+        export PATH="${toolshim}:$(brew --prefix)/bin:${PATH}"
 
-        make SHELL=/bin/bash
+        which gcc
+        gcc --version
+        make SHELL=/bin/bash CC=gcc CXX=g++ FC=gfortran
 
     - name: Upload binary
       uses: actions/upload-artifact@v4

From 27fd8ae5e9706d1c8ee907930bcd234f9e8aa940 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 13:38:25 +0200
Subject: [PATCH 50/69] CI: build macOS ARM deps from my_lib READMEs

---
 .github/workflows/compile_madng.yml | 83 ++++++++++++++++++++++++-----
 1 file changed, 71 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 8b60b37..2ffee33 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -107,30 +107,89 @@ jobs:
           -e "s#-mfma##g" \
           MAD/src/Makefile
 
-    - name: Rebuild macOS ARM static dependencies
+    - name: Build MAD-NG dependencies (README order)
       run: |
+        set -euo pipefail
+
         gcc_prefix="$(brew --prefix gcc)"
         gcc_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gcc-*' ! -name 'gcc-ar*' ! -name 'gcc-nm*' ! -name 'gcc-ranlib*' | sort | tail -n1)"
         gxx_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'g++-*' | sort | tail -n1)"
         gfortran_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gfortran-*' | sort | tail -n1)"
         test -n "${gcc_bin}" && test -n "${gxx_bin}" && test -n "${gfortran_bin}"
+
         toolshim="${RUNNER_TEMP}/gcc-shim"
         mkdir -p "${toolshim}"
         ln -sf "${gcc_bin}" "${toolshim}/gcc"
         ln -sf "${gxx_bin}" "${toolshim}/g++"
         ln -sf "${gfortran_bin}" "${toolshim}/gfortran"
-        brew_bin="$(brew --prefix)/bin"
-        PATH="${toolshim}:${brew_bin}:${PATH}" \
-          JOBS="$(sysctl -n hw.ncpu)" \
-          CC=gcc CXX=g++ FC=gfortran AR=ar RANLIB=ranlib \
-          ./tools/build_madng_deps_macos.sh
+        export PATH="${toolshim}:$(brew --prefix)/bin:${PATH}"
 
-    - name: Stage MAD-NG headers
-      run: |
-        mkdir -p MAD/tools
-        cp -f tools/stage_madng_headers_macos.sh MAD/tools/
-        chmod +x MAD/tools/stage_madng_headers_macos.sh
-        (cd MAD && ./tools/stage_madng_headers_macos.sh)
+        export OS=macosx
+        export MACOSX_DEPLOYMENT_TARGET=11
+        export JOBS="$(sysctl -n hw.ncpu)"
+
+        mkdir -p MAD/bin/macosx
+
+        cd MAD/my_lib
+
+        echo "== LuaJIT (README.luajit) =="
+        cd luajit
+        make clean
+        make -j"${JOBS}" amalg PREFIX="$(pwd)"
+        make install PREFIX="$(pwd)"
+        cp -f src/libluajit.a ../../bin/macosx/
+        cd ..
+
+        echo "== LFS (README.lfs) =="
+        cd lfs
+        make clean || true
+        make lfs.a
+        cp -f liblfs.a ../../bin/macosx/
+        cd ..
+
+        echo "== LPEG (README.lpeg) =="
+        cd lpeg
+        make clean || true
+        make macosx
+        cp -f liblpeg.a ../../bin/macosx/
+        cd ..
+
+        echo "== LAPACK (README.lapack) =="
+        cd lapack
+        cp -f make.inc.example make.inc
+        make clean || true
+        make -j"${JOBS}" lib
+        cp -f liblapack.a librefblas.a ../../bin/macosx/
+        cd ..
+
+        echo "== FFTW3 (README.fftw3) =="
+        cd fftw3
+        make clean || true
+        ./configure --disable-shared
+        make -j"${JOBS}"
+        cp -f .libs/libfftw3.a ../../bin/macosx/
+        cd ..
+
+        echo "== NFFT3 (README.nfft3) =="
+        cd nfft3
+        make clean || true
+        ./configure --enable-all --disable-shared \
+          --with-fftw3="$(pwd)"/../fftw3 \
+          --with-fftw3-libdir="$(pwd)"/../fftw3/.libs \
+          --with-fftw3-includedir="$(pwd)"/../fftw3/api
+        make -j"${JOBS}"
+        cp -f .libs/libnfft3.a ../../bin/macosx/
+        cd ..
+
+        echo "== NLOPT (README.nlopt) =="
+        cd nlopt
+        rm -rf build
+        mkdir -p build
+        cd build
+        cmake -DBUILD_SHARED_LIBS=OFF -DNLOPT_CXX=OFF ..
+        make -j"${JOBS}"
+        cp -f libnlopt.a ../../../bin/macosx/
+        cd ../..
 
     - name: Compile MAD-NG
       working-directory: MAD/src

From c5c127ae837abf592d11bdc0c720b9128247f1ef Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 13:42:33 +0200
Subject: [PATCH 51/69] print toolchain

---
 .github/workflows/compile_madng.yml | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 2ffee33..53c8e95 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -124,6 +124,14 @@ jobs:
         ln -sf "${gfortran_bin}" "${toolshim}/gfortran"
         export PATH="${toolshim}:$(brew --prefix)/bin:${PATH}"
 
+        echo "== Toolchain =="
+        which gcc
+        gcc --version
+        which g++
+        g++ --version
+        which gfortran
+        gfortran --version
+
         export OS=macosx
         export MACOSX_DEPLOYMENT_TARGET=11
         export JOBS="$(sysctl -n hw.ncpu)"
@@ -206,8 +214,13 @@ jobs:
         ln -sf "${gfortran_bin}" "${toolshim}/gfortran"
         export PATH="${toolshim}:$(brew --prefix)/bin:${PATH}"
 
+        echo "== Toolchain =="
         which gcc
         gcc --version
+        which g++
+        g++ --version
+        which gfortran
+        gfortran --version
         make SHELL=/bin/bash CC=gcc CXX=g++ FC=gfortran
 
     - name: Upload binary

From ead7f47f64aa04fe10228c0a21ad259afca93884 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 13:45:17 +0200
Subject: [PATCH 52/69] my_lib -> lib

---
 .github/workflows/compile_madng.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 53c8e95..70ad775 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -138,7 +138,8 @@ jobs:
 
         mkdir -p MAD/bin/macosx
 
-        cd MAD/my_lib
+        # MAD-NG repo vendors third-party deps under MAD/lib (checked out with submodules).
+        cd MAD/lib
 
         echo "== LuaJIT (README.luajit) =="
         cd luajit

From 554230f8e85b66a64a420698e62f5141c12148bd Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 13:49:50 +0200
Subject: [PATCH 53/69] force gcc 13

---
 .github/workflows/compile_madng.yml | 34 +++++++++++++++++++----------
 1 file changed, 22 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 70ad775..4af90c0 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -91,7 +91,8 @@ jobs:
     - name: Install dependencies
       run: |
         brew update
-        brew install gcc make cmake automake libtool pkg-config
+        # Pin GCC major to avoid runner drift.
+        brew install gcc@13 make cmake automake libtool pkg-config
 
     - name: Select Makefile
       run: |
@@ -111,11 +112,11 @@ jobs:
       run: |
         set -euo pipefail
 
-        gcc_prefix="$(brew --prefix gcc)"
-        gcc_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gcc-*' ! -name 'gcc-ar*' ! -name 'gcc-nm*' ! -name 'gcc-ranlib*' | sort | tail -n1)"
-        gxx_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'g++-*' | sort | tail -n1)"
-        gfortran_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gfortran-*' | sort | tail -n1)"
-        test -n "${gcc_bin}" && test -n "${gxx_bin}" && test -n "${gfortran_bin}"
+        gcc_prefix="$(brew --prefix gcc@13)"
+        gcc_bin="${gcc_prefix}/bin/gcc-13"
+        gxx_bin="${gcc_prefix}/bin/g++-13"
+        gfortran_bin="${gcc_prefix}/bin/gfortran-13"
+        test -x "${gcc_bin}" && test -x "${gxx_bin}" && test -x "${gfortran_bin}"
 
         toolshim="${RUNNER_TEMP}/gcc-shim"
         mkdir -p "${toolshim}"
@@ -140,9 +141,18 @@ jobs:
 
         # MAD-NG repo vendors third-party deps under MAD/lib (checked out with submodules).
         cd MAD/lib
+        echo "== MAD/lib contents =="
+        ls -la
 
         echo "== LuaJIT (README.luajit) =="
-        cd luajit
+        if [[ -d "luajit" ]]; then
+          cd luajit
+        elif [[ -d "LuaJIT" ]]; then
+          cd LuaJIT
+        else
+          echo "LuaJIT directory not found under MAD/lib"
+          exit 1
+        fi
         make clean
         make -j"${JOBS}" amalg PREFIX="$(pwd)"
         make install PREFIX="$(pwd)"
@@ -203,11 +213,11 @@ jobs:
     - name: Compile MAD-NG
       working-directory: MAD/src
       run: |
-        gcc_prefix="$(brew --prefix gcc)"
-        gcc_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gcc-*' ! -name 'gcc-ar*' ! -name 'gcc-nm*' ! -name 'gcc-ranlib*' | sort | tail -n1)"
-        gxx_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'g++-*' | sort | tail -n1)"
-        gfortran_bin="$(find "${gcc_prefix}/bin" -maxdepth 1 -type f -name 'gfortran-*' | sort | tail -n1)"
-        test -n "${gcc_bin}" && test -n "${gxx_bin}" && test -n "${gfortran_bin}"
+        gcc_prefix="$(brew --prefix gcc@13)"
+        gcc_bin="${gcc_prefix}/bin/gcc-13"
+        gxx_bin="${gcc_prefix}/bin/g++-13"
+        gfortran_bin="${gcc_prefix}/bin/gfortran-13"
+        test -x "${gcc_bin}" && test -x "${gxx_bin}" && test -x "${gfortran_bin}"
         toolshim="${RUNNER_TEMP}/gcc-shim"
         mkdir -p "${toolshim}"
         ln -sf "${gcc_bin}" "${toolshim}/gcc"

From af6c50a0c2bc50d37bf57ee4bb91583b6d50f775 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 13:50:04 +0200
Subject: [PATCH 54/69] Delete old sh files

---
 tools/build_madng_deps_macos.sh    | 320 -----------------------------
 tools/stage_madng_headers_macos.sh | 207 -------------------
 2 files changed, 527 deletions(-)
 delete mode 100755 tools/build_madng_deps_macos.sh
 delete mode 100755 tools/stage_madng_headers_macos.sh

diff --git a/tools/build_madng_deps_macos.sh b/tools/build_madng_deps_macos.sh
deleted file mode 100755
index 7a9f1ee..0000000
--- a/tools/build_madng_deps_macos.sh
+++ /dev/null
@@ -1,320 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-
-# Builds MAD-NG third-party *static* libraries into: ./bin/macosx
-#
-# You still need system build tools. Typical (Homebrew) prerequisites:
-#   brew install cmake gcc make automake libtool pkg-config
-#
-# Example:
-#   ./tools/build_madng_deps_macos.sh
-
-ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
-OS_TAG="macosx"
-BIN_DIR="${ROOT}/bin/${OS_TAG}"
-LIB_DIR="${ROOT}/lib"
-
-JOBS="${JOBS:-}"
-CC="${CC:-}"
-CXX="${CXX:-}"
-FC="${FC:-}"
-AR="${AR:-}"
-RANLIB="${RANLIB:-}"
-
-MACOSX_DEPLOYMENT_TARGET="${MACOSX_DEPLOYMENT_TARGET:-11.0}"
-
-LUAJIT_REF="${LUAJIT_REF:-mad-patch}"
-LUAJIT_REPO="${LUAJIT_REPO:-https://github.com/MethodicalAcceleratorDesign/LuaJIT.git}"
-
-LFS_REF="${LFS_REF:-}"
-LFS_REPO="${LFS_REPO:-https://github.com/MethodicalAcceleratorDesign/luafilesystem.git}"
-
-LPEG_VERSION="${LPEG_VERSION:-1.1.0}"
-FFTW_VERSION="${FFTW_VERSION:-3.3.10}"
-NFFT_VERSION="${NFFT_VERSION:-3.5.3}"
-NLOPT_REF="${NLOPT_REF:-v2.9.1}"
-LAPACK_REF="${LAPACK_REF:-v3.12.1}"
-
-prompt_default() {
-  local var_name="$1"
-  local prompt="$2"
-  local default="$3"
-  local current="${!var_name:-}"
-  if [[ -n "${current}" ]]; then
-    return 0
-  fi
-  local reply=""
-  read -r -p "${prompt} [${default}]: " reply || true
-  if [[ -z "${reply}" ]]; then
-    reply="${default}"
-  fi
-  printf -v "${var_name}" "%s" "${reply}"
-}
-
-need_cmd() {
-  command -v "$1" >/dev/null 2>&1 || {
-    echo "Missing required command: $1" >&2
-    exit 1
-  }
-}
-
-sedi() {
-  # Portable in-place sed across GNU/BSD
-  if sed --version >/dev/null 2>&1; then
-    sed -i "$@"
-  else
-    sed -i '' "$@"
-  fi
-}
-
-fetch_tarball() {
-  local url="$1"
-  local out="$2"
-  if [[ -f "${out}" ]]; then
-    return 0
-  fi
-  if command -v curl >/dev/null 2>&1; then
-    curl -L --fail "${url}" -o "${out}"
-  else
-    need_cmd wget
-    wget -O "${out}" "${url}"
-  fi
-}
-
-ensure_dirs() {
-  mkdir -p "${BIN_DIR}"
-  mkdir -p "${LIB_DIR}"
-}
-
-build_luajit() {
-  echo "== LuaJIT (${LUAJIT_REF}) =="
-  need_cmd git
-  need_cmd make
-
-  local dir="${LIB_DIR}/luajit"
-  if [[ ! -d "${dir}/.git" ]]; then
-    git clone "${LUAJIT_REPO}" "${dir}"
-  fi
-  ( export MACOSX_DEPLOYMENT_TARGET
-    cd "${dir}"
-    git fetch --all --tags
-    git checkout "${LUAJIT_REF}"
-    git pull --ff-only || true
-    make clean
-    make -j"${JOBS}" amalg PREFIX="$(pwd)"
-    make install PREFIX="$(pwd)"
-    cp -f src/libluajit.a "${BIN_DIR}/libluajit.a"
-  )
-}
-
-build_lfs() {
-  echo "== LuaFileSystem ${LFS_REF:+(${LFS_REF})} =="
-  need_cmd git
-  need_cmd make
-
-  local dir="${LIB_DIR}/lfs"
-  if [[ ! -d "${dir}/.git" ]]; then
-    git clone "${LFS_REPO}" "${dir}"
-  fi
-  ( cd "${dir}"
-    git fetch --all --tags
-    git pull --ff-only || true
-    if [[ -n "${LFS_REF}" ]]; then
-      git checkout "${LFS_REF}" || git checkout -B "${LFS_REF}" "origin/${LFS_REF}"
-    fi
-    make clean || true
-    make -j"${JOBS}" AR="${AR}" lfs.a
-    cp -f liblfs.a "${BIN_DIR}/liblfs.a"
-  )
-}
-
-build_lpeg() {
-  echo "== LPeg (${LPEG_VERSION}) =="
-  need_cmd make
-  need_cmd ar
-
-  local tar="lpeg-${LPEG_VERSION}.tar.gz"
-  local url="http://www.inf.puc-rio.br/~roberto/lpeg/${tar}"
-  local tar_path="${LIB_DIR}/${tar}"
-  local src_dir="${LIB_DIR}/lpeg-${LPEG_VERSION}"
-  local dir="${LIB_DIR}/lpeg"
-
-  if [[ ! -d "${src_dir}" ]]; then
-    fetch_tarball "${url}" "${tar_path}"
-    ( cd "${LIB_DIR}" && tar xzf "${tar}" )
-  fi
-  if [[ ! -e "${dir}" ]]; then
-    ln -s "lpeg-${LPEG_VERSION}" "${dir}"
-  fi
-
-  local luajit_inc="${LIB_DIR}/luajit/include/luajit-2.1"
-  local luajit_lib="${LIB_DIR}/luajit/lib/libluajit-5.1.a"
-  if [[ ! -f "${luajit_lib}" ]]; then
-    echo "LuaJIT static library not found at ${luajit_lib}" >&2
-    echo "Run LuaJIT step first (or adjust paths)." >&2
-    exit 1
-  fi
-
-  ( cd "${dir}"
-    if [[ ! -f makefile.mad.orig ]]; then
-      cp -f makefile makefile.mad.orig
-    else
-      cp -f makefile.mad.orig makefile
-    fi
-    sedi \
-      -e "s|^[#[:space:]]*LUADIR[[:space:]]*=.*|LUADIR = ${luajit_inc}|" \
-      -e "s|^[#[:space:]]*LUALIB[[:space:]]*=.*|LUALIB = ${luajit_lib}|" \
-      -e "s|^[#[:space:]]*COPT[[:space:]]*=.*|COPT = -O3|" \
-      makefile
-    make clean || true
-    make -j"${JOBS}" CC="${CC}" LUADIR="${luajit_inc}" lpvm.o lpcap.o lptree.o lpcode.o lpprint.o lpcset.o
-    "${AR}" -r liblpeg.a lpvm.o lpcap.o lptree.o lpcode.o lpprint.o lpcset.o
-    "${RANLIB}" liblpeg.a
-    cp -f liblpeg.a "${BIN_DIR}/liblpeg.a"
-  )
-}
-
-build_lapack() {
-  echo "== LAPACK (${LAPACK_REF}) =="
-  need_cmd git
-  need_cmd make
-
-  local dir="${LIB_DIR}/lapack"
-  if [[ ! -d "${dir}/.git" ]]; then
-    git clone https://github.com/Reference-LAPACK/lapack "${dir}"
-  fi
-  ( cd "${dir}"
-    git fetch --all --tags
-    git checkout "${LAPACK_REF}"
-    cp -f make.inc.example make.inc
-    sedi \
-      -e 's/^\(CFLAGS[[:space:]]*=[[:space:]]*.*\)$/\1 -fPIC/' \
-      -e 's/^\(FFLAGS[[:space:]]*=[[:space:]]*.*\)$/\1 -fPIC/' \
-      -e 's/^\(FFLAGS_NOOPT[[:space:]]*=[[:space:]]*.*\)$/\1 -fPIC/' \
-      make.inc || true
-    make clean
-    make -j"${JOBS}" blaslib
-    make -j"${JOBS}" lapacklib
-    cp -f librefblas.a "${BIN_DIR}/librefblas.a"
-    cp -f liblapack.a "${BIN_DIR}/liblapack.a"
-  )
-}
-
-build_fftw3() {
-  echo "== FFTW3 (${FFTW_VERSION}) =="
-  need_cmd make
-
-  local tar="fftw-${FFTW_VERSION}.tar.gz"
-  local url="https://fftw.org/${tar}"
-  local tar_path="${LIB_DIR}/${tar}"
-  local src_dir="${LIB_DIR}/fftw-${FFTW_VERSION}"
-  local dir="${LIB_DIR}/fftw3"
-
-  if [[ ! -d "${src_dir}" ]]; then
-    fetch_tarball "${url}" "${tar_path}"
-    ( cd "${LIB_DIR}" && tar xzf "${tar}" )
-  fi
-  if [[ ! -e "${dir}" ]]; then
-    ln -s "fftw-${FFTW_VERSION}" "${dir}"
-  fi
-
-  ( cd "${dir}"
-    ./configure --disable-shared CC="${CC}"
-    make clean || true
-    make -j"${JOBS}"
-    cp -f .libs/libfftw3.a "${BIN_DIR}/libfftw3.a"
-  )
-}
-
-build_nfft3() {
-  echo "== NFFT3 (${NFFT_VERSION}) =="
-  need_cmd make
-
-  local tar="nfft-${NFFT_VERSION}.tar.gz"
-  local url="https://www-user.tu-chemnitz.de/~potts/nfft/download/${tar}"
-  local tar_path="${LIB_DIR}/${tar}"
-  local src_dir="${LIB_DIR}/nfft-${NFFT_VERSION}"
-  local dir="${LIB_DIR}/nfft3"
-
-  if [[ ! -d "${src_dir}" ]]; then
-    fetch_tarball "${url}" "${tar_path}"
-    ( cd "${LIB_DIR}" && tar xzf "${tar}" )
-  fi
-  if [[ ! -e "${dir}" ]]; then
-    ln -s "nfft-${NFFT_VERSION}" "${dir}"
-  fi
-
-  ( cd "${dir}"
-    make distclean || true
-    ./configure --disable-shared \
-      --with-fftw3="$(pwd)/../fftw3" \
-      --with-fftw3-libdir="$(pwd)/../fftw3/.libs" \
-      --with-fftw3-includedir="$(pwd)/../fftw3/api" \
-      CC="${CC}"
-    # Only build the library — strip applications/examples/tests from SUBDIRS.
-    sed -i.bak 's/^\(SUBDIRS[[:space:]]*=\).*/\1 include kernel/' Makefile
-    make -j"${JOBS}"
-    cp -f .libs/libnfft3.a "${BIN_DIR}/libnfft3.a"
-  )
-}
-
-build_nlopt() {
-  echo "== NLOpt (${NLOPT_REF}) =="
-  need_cmd git
-  need_cmd cmake
-  need_cmd make
-
-  local dir="${LIB_DIR}/nlopt"
-  if [[ ! -d "${dir}/.git" ]]; then
-    git clone https://github.com/stevengj/nlopt "${dir}"
-  fi
-
-  ( cd "${dir}"
-    git fetch --all --tags
-    git checkout "${NLOPT_REF}"
-    rm -rf build
-    mkdir -p build
-    cd build
-    cmake -DBUILD_SHARED_LIBS=OFF -DNLOPT_CXX=OFF -DCMAKE_C_COMPILER="${CC}" \
-      -DCMAKE_POLICY_VERSION_MINIMUM=3.5 ..
-    make -j"${JOBS}"
-    cp -f libnlopt.a "${BIN_DIR}/libnlopt.a"
-  )
-}
-
-main() {
-  ensure_dirs
-
-  prompt_default JOBS "Parallel jobs (make -j)" "$(sysctl -n hw.ncpu 2>/dev/null || echo 4)"
-  prompt_default CC "C compiler (CC)" "clang"
-  prompt_default CXX "C++ compiler (CXX)" "clang++"
-  prompt_default FC "Fortran compiler (FC)" "gfortran"
-  prompt_default AR "Archiver (AR)" "ar"
-  prompt_default RANLIB "RANLIB" "ranlib"
-
-  need_cmd "${CC}"
-  need_cmd "${FC}"
-  need_cmd "${AR}"
-  need_cmd "${RANLIB}"
-  need_cmd tar
-
-  echo "Root: ${ROOT}"
-  echo "Lib sources: ${LIB_DIR}"
-  echo "Output: ${BIN_DIR}"
-  echo "MACOSX_DEPLOYMENT_TARGET: ${MACOSX_DEPLOYMENT_TARGET}"
-  echo
-
-  build_luajit
-  build_lfs
-  build_lpeg
-  build_lapack
-  build_fftw3
-  build_nfft3
-  build_nlopt
-
-  echo
-  echo "Done. Built libraries in: ${BIN_DIR}"
-  ls -1 "${BIN_DIR}"
-}
-
-main "$@"
diff --git a/tools/stage_madng_headers_macos.sh b/tools/stage_madng_headers_macos.sh
deleted file mode 100755
index af1a62a..0000000
--- a/tools/stage_madng_headers_macos.sh
+++ /dev/null
@@ -1,207 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-
-# Stage headers into the layout expected by MAD-NG's unmodified `src/Makefile`.
-# The fetch/stage layout follows the documented MAD dependency build flow.
-#
-# Expected include paths (from `src/Makefile`):
-#   -I../lib/luajit/src            -> lua.h, luajit.h, etc
-#   -I../lib/nlopt/src/api         -> nlopt.h
-#   -I../lib/fftw3/api             -> fftw3.h
-#   -I../lib/nfft3/include         -> nfft3.h
-#
-# This script does NOT build archives; it only ensures headers exist (by
-# downloading sources, or by symlinking/copying from user-provided locations).
-
-ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
-LIB_DIR="${ROOT}/lib"
-LUAJIT_REF="${LUAJIT_REF:-mad-patch}"
-LUAJIT_REPO="${LUAJIT_REPO:-https://github.com/MethodicalAcceleratorDesign/LuaJIT.git}"
-
-NLOPT_REF="${NLOPT_REF:-v2.7.1}"
-NLOPT_REPO="${NLOPT_REPO:-https://github.com/stevengj/nlopt.git}"
-
-FFTW_VERSION="${FFTW_VERSION:-3.3.10}"
-NFFT_VERSION="${NFFT_VERSION:-3.5.3}"
-
-# Optional: point these at already-installed headers (will be copied/symlinked)
-LUAJIT_SRC_DIR="${LUAJIT_SRC_DIR:-}"   # directory containing lua.h, luajit.h, etc
-NLOPT_INC_DIR="${NLOPT_INC_DIR:-}"     # directory containing nlopt.h
-FFTW_INC_DIR="${FFTW_INC_DIR:-}"       # directory containing fftw3.h
-NFFT_INC_DIR="${NFFT_INC_DIR:-}"       # directory containing nfft3.h
-
-need_cmd() {
-  command -v "$1" >/dev/null 2>&1 || { echo "Missing command: $1" >&2; exit 1; }
-}
-
-pick_make() {
-  if command -v gmake >/dev/null 2>&1; then
-    echo "gmake"
-  else
-    echo "make"
-  fi
-}
-
-fetch_tarball() {
-  local url="$1"
-  local out="$2"
-  if [[ -f "${out}" ]]; then return 0; fi
-  if command -v curl >/dev/null 2>&1; then
-    curl -L --fail "${url}" -o "${out}"
-  else
-    need_cmd wget
-    wget -O "${out}" "${url}"
-  fi
-}
-
-stage_dir_copy_or_link() {
-  local src="$1"
-  local dest="$2"
-  local mode="${3:-symlink}" # symlink|copy
-  rm -rf "${dest}"
-  mkdir -p "$(dirname "${dest}")"
-  case "${mode}" in
-    symlink) ln -s "${src}" "${dest}" ;;
-    copy) cp -a "${src}" "${dest}" ;;
-    *) echo "Unknown mode: ${mode}" >&2; exit 1 ;;
-  esac
-}
-
-stage_file_copy_or_link() {
-  local src="$1"
-  local dest="$2"
-  local mode="${3:-symlink}" # symlink|copy
-  rm -f "${dest}"
-  mkdir -p "$(dirname "${dest}")"
-  case "${mode}" in
-    symlink) ln -s "${src}" "${dest}" ;;
-    copy) cp -a "${src}" "${dest}" ;;
-    *) echo "Unknown mode: ${mode}" >&2; exit 1 ;;
-  esac
-}
-
-main() {
-  mkdir -p "${LIB_DIR}"
-
-  # LuaJIT headers -> lib/luajit/src/*
-  if [[ -n "${LUAJIT_SRC_DIR}" ]]; then
-    echo "Staging LuaJIT headers from LUAJIT_SRC_DIR=${LUAJIT_SRC_DIR}"
-    [[ -e "${LUAJIT_SRC_DIR}/lua.h" ]] || { echo "Missing ${LUAJIT_SRC_DIR}/lua.h" >&2; exit 1; }
-    [[ -e "${LUAJIT_SRC_DIR}/luajit.h" ]] || { echo "Missing ${LUAJIT_SRC_DIR}/luajit.h" >&2; exit 1; }
-    mkdir -p "${LIB_DIR}/luajit"
-    stage_dir_copy_or_link "${LUAJIT_SRC_DIR}" "${LIB_DIR}/luajit/src" "symlink"
-  else
-    echo "Fetching LuaJIT repo for headers (${LUAJIT_REF})"
-    need_cmd git
-    local_dir="${LIB_DIR}/luajit"
-    if [[ ! -d "${local_dir}/.git" ]]; then
-      git clone "${LUAJIT_REPO}" "${local_dir}"
-    fi
-    ( cd "${local_dir}"
-      git fetch --all --tags
-      git checkout "${LUAJIT_REF}"
-      git pull --ff-only || true
-    )
-
-    # Follow `README.luajit` literally enough to materialize `src/luajit.h`:
-    #   export MACOSX_DEPLOYMENT_TARGET=11
-    #   make clean
-    #   make amalg PREFIX=`pwd`
-    #   make install PREFIX=`pwd`
-    if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
-      echo "luajit.h not in repo — building LuaJIT as documented by MAD..."
-      mk="$(pick_make)"
-      (
-        cd "${local_dir}"
-        export MACOSX_DEPLOYMENT_TARGET="${MACOSX_DEPLOYMENT_TARGET:-11}"
-        "${mk}" clean
-        "${mk}" amalg PREFIX="$(pwd)"
-        "${mk}" install PREFIX="$(pwd)"
-      )
-    fi
-  fi
-
-  # NLOpt headers -> lib/nlopt/src/api/nlopt.h
-  if [[ -n "${NLOPT_INC_DIR}" ]]; then
-    echo "Staging NLOpt header from NLOPT_INC_DIR=${NLOPT_INC_DIR}"
-    stage_file_copy_or_link "${NLOPT_INC_DIR}/nlopt.h" "${LIB_DIR}/nlopt/src/api/nlopt.h" "symlink"
-  else
-    echo "Fetching NLOpt repo for headers (${NLOPT_REF})"
-    need_cmd git
-    local_dir="${LIB_DIR}/nlopt"
-    if [[ ! -d "${local_dir}/.git" ]]; then
-      git clone "${NLOPT_REPO}" "${local_dir}"
-    fi
-    ( cd "${local_dir}"
-      git fetch --all --tags
-      git checkout "${NLOPT_REF}"
-      git pull --ff-only 2>/dev/null || true
-    )
-  fi
-
-  # FFTW headers -> lib/fftw3/api/fftw3.h
-  if [[ -n "${FFTW_INC_DIR}" ]]; then
-    echo "Staging FFTW header from FFTW_INC_DIR=${FFTW_INC_DIR}"
-    stage_file_copy_or_link "${FFTW_INC_DIR}/fftw3.h" "${LIB_DIR}/fftw3/api/fftw3.h" "symlink"
-  else
-    echo "Fetching FFTW tarball for headers (${FFTW_VERSION})"
-    need_cmd tar
-    tar_name="fftw-${FFTW_VERSION}.tar.gz"
-    tar_path="${LIB_DIR}/${tar_name}"
-    url="https://fftw.org/${tar_name}"
-    fetch_tarball "${url}" "${tar_path}"
-    ( cd "${LIB_DIR}" && tar xzf "${tar_name}" )
-    rm -rf "${LIB_DIR}/fftw3"
-    mkdir -p "${LIB_DIR}/fftw3/api"
-    if [[ -e "${LIB_DIR}/fftw-${FFTW_VERSION}/api/fftw3.h" ]]; then
-      ln -s "${LIB_DIR}/fftw-${FFTW_VERSION}/api/fftw3.h" "${LIB_DIR}/fftw3/api/fftw3.h"
-    else
-      ln -s "${LIB_DIR}/fftw-${FFTW_VERSION}/fftw3.h" "${LIB_DIR}/fftw3/api/fftw3.h"
-    fi
-  fi
-
-  # NFFT headers -> lib/nfft3/include/nfft3.h
-  if [[ -n "${NFFT_INC_DIR}" ]]; then
-    echo "Staging NFFT header(s) from NFFT_INC_DIR=${NFFT_INC_DIR}"
-    mkdir -p "${LIB_DIR}/nfft3"
-    stage_dir_copy_or_link "${NFFT_INC_DIR}" "${LIB_DIR}/nfft3/include" "symlink"
-  else
-    echo "Fetching NFFT tarball for headers (${NFFT_VERSION})"
-    need_cmd tar
-    tar_name="nfft-${NFFT_VERSION}.tar.gz"
-    tar_path="${LIB_DIR}/${tar_name}"
-    url="https://www-user.tu-chemnitz.de/~potts/nfft/download/${tar_name}"
-    fetch_tarball "${url}" "${tar_path}"
-    ( cd "${LIB_DIR}" && tar xzf "${tar_name}" )
-    rm -rf "${LIB_DIR}/nfft3"
-    mkdir -p "${LIB_DIR}/nfft3/include"
-    if [[ -d "${LIB_DIR}/nfft-${NFFT_VERSION}/include" ]]; then
-      for header in "${LIB_DIR}"/nfft-"${NFFT_VERSION}"/include/*; do
-        ln -s "${header}" "${LIB_DIR}/nfft3/include/$(basename "${header}")"
-      done
-    else
-      ln -s "${LIB_DIR}/nfft-${NFFT_VERSION}/nfft3.h" "${LIB_DIR}/nfft3/include/nfft3.h"
-    fi
-  fi
-
-  echo
-  echo "Header checks (expected by src/Makefile):"
-  local rc=0
-  for f in \
-    "${LIB_DIR}/luajit/src/lua.h" \
-    "${LIB_DIR}/luajit/src/luajit.h" \
-    "${LIB_DIR}/nlopt/src/api/nlopt.h" \
-    "${LIB_DIR}/fftw3/api/fftw3.h" \
-    "${LIB_DIR}/nfft3/include/nfft3.h"
-  do
-    if [[ -e "${f}" ]]; then
-      echo "  OK  ${f}"
-    else
-      echo "  MISS ${f}" >&2
-      rc=1
-    fi
-  done
-  return "${rc}"
-}
-
-main "$@"

From 542a98fbe1fea6596631349396c7c373aaea8f2e Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 13:54:20 +0200
Subject: [PATCH 55/69] Download dependancies first

---
 .github/workflows/compile_madng.yml | 31 +++++++++++++++++++++--------
 1 file changed, 23 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 4af90c0..7ea9d2f 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -145,14 +145,11 @@ jobs:
         ls -la
 
         echo "== LuaJIT (README.luajit) =="
-        if [[ -d "luajit" ]]; then
-          cd luajit
-        elif [[ -d "LuaJIT" ]]; then
-          cd LuaJIT
-        else
-          echo "LuaJIT directory not found under MAD/lib"
-          exit 1
-        fi
+        rm -rf luajit
+        git clone https://github.com/MethodicalAcceleratorDesign/LuaJIT.git luajit
+        cd luajit
+        git checkout mad-patch
+        git pull
         make clean
         make -j"${JOBS}" amalg PREFIX="$(pwd)"
         make install PREFIX="$(pwd)"
@@ -160,6 +157,8 @@ jobs:
         cd ..
 
         echo "== LFS (README.lfs) =="
+        rm -rf lfs
+        git clone https://github.com/MethodicalAcceleratorDesign/luafilesystem.git lfs
         cd lfs
         make clean || true
         make lfs.a
@@ -167,6 +166,10 @@ jobs:
         cd ..
 
         echo "== LPEG (README.lpeg) =="
+        rm -rf lpeg lpeg-1.1.0 lpeg-1.1.0.tar.gz
+        curl -fsSL -o lpeg-1.1.0.tar.gz http://www.inf.puc-rio.br/~roberto/lpeg/lpeg-1.1.0.tar.gz
+        tar xvzf lpeg-1.1.0.tar.gz
+        ln -s lpeg-1.1.0 lpeg
         cd lpeg
         make clean || true
         make macosx
@@ -174,6 +177,8 @@ jobs:
         cd ..
 
         echo "== LAPACK (README.lapack) =="
+        rm -rf lapack
+        git clone https://github.com/Reference-LAPACK/lapack lapack
         cd lapack
         cp -f make.inc.example make.inc
         make clean || true
@@ -182,6 +187,10 @@ jobs:
         cd ..
 
         echo "== FFTW3 (README.fftw3) =="
+        rm -rf fftw3 fftw-3.3.10 fftw-3.3.10.tar.gz
+        curl -fsSL -o fftw-3.3.10.tar.gz ftp://ftp.fftw.org/pub/fftw/fftw-3.3.10.tar.gz
+        tar xvzf fftw-3.3.10.tar.gz
+        ln -s fftw-3.3.10 fftw3
         cd fftw3
         make clean || true
         ./configure --disable-shared
@@ -190,6 +199,10 @@ jobs:
         cd ..
 
         echo "== NFFT3 (README.nfft3) =="
+        rm -rf nfft3 nfft-3.5.3 nfft-3.5.3.tar.gz
+        curl -fsSL -o nfft-3.5.3.tar.gz http://www.nfft.org/download/nfft-3.5.3.tar.gz
+        tar xvzf nfft-3.5.3.tar.gz
+        ln -s nfft-3.5.3 nfft3
         cd nfft3
         make clean || true
         ./configure --enable-all --disable-shared \
@@ -201,6 +214,8 @@ jobs:
         cd ..
 
         echo "== NLOPT (README.nlopt) =="
+        rm -rf nlopt
+        git clone https://github.com/stevengj/nlopt nlopt
         cd nlopt
         rm -rf build
         mkdir -p build

From 869426b22dfc6342079379a53afff18c4e8b8bc3 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 13:58:24 +0200
Subject: [PATCH 56/69] Make the edits to the files

---
 .github/workflows/compile_madng.yml | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 7ea9d2f..8e28696 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -171,6 +171,13 @@ jobs:
         tar xvzf lpeg-1.1.0.tar.gz
         ln -s lpeg-1.1.0 lpeg
         cd lpeg
+        # Apply README.lpeg edits.
+        sed -i.bak \
+          -e 's#^#\\?LUADIR[[:space:]]*=.*#LUADIR = ../luajit/include/luajit-2.1#g' \
+          -e 's#^LUALIB[[:space:]]*=.*#LUALIB = ../luajit/lib/libluajit-5.1.a#g' \
+          -e 's#^COPT[[:space:]]*=.*#COPT = -O3 -DNDEBUG#g' \
+          makefile || true
+        rm -f makefile.bak || true
         make clean || true
         make macosx
         cp -f liblpeg.a ../../bin/macosx/
@@ -181,6 +188,13 @@ jobs:
         git clone https://github.com/Reference-LAPACK/lapack lapack
         cd lapack
         cp -f make.inc.example make.inc
+        # Apply README.lapack edits: add -fPIC to CFLAGS/FFLAGS/FFLAGS_NOOPT.
+        sed -i.bak -E \
+          -e 's#^(CFLAGS[[:space:]]*=[[:space:]]*)#\\1-fPIC #g' \
+          -e 's#^(FFLAGS[[:space:]]*=[[:space:]]*)#\\1-fPIC #g' \
+          -e 's#^(FFLAGS_NOOPT[[:space:]]*=[[:space:]]*)#\\1-fPIC #g' \
+          make.inc || true
+        rm -f make.inc.bak || true
         make clean || true
         make -j"${JOBS}" lib
         cp -f liblapack.a librefblas.a ../../bin/macosx/
@@ -200,7 +214,8 @@ jobs:
 
         echo "== NFFT3 (README.nfft3) =="
         rm -rf nfft3 nfft-3.5.3 nfft-3.5.3.tar.gz
-        curl -fsSL -o nfft-3.5.3.tar.gz http://www.nfft.org/download/nfft-3.5.3.tar.gz
+        # README.nfft3 points to nfft.org; the upstream host also serves the tarball from TU Chemnitz.
+        curl -fsSL -o nfft-3.5.3.tar.gz https://www-user.tu-chemnitz.de/~potts/nfft/download/nfft-3.5.3.tar.gz
         tar xvzf nfft-3.5.3.tar.gz
         ln -s nfft-3.5.3 nfft3
         cd nfft3

From 0ec1d165de2fbb00e5d65fa0f50ed15b9249d44d Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 14:03:12 +0200
Subject: [PATCH 57/69] fix sed

---
 .github/workflows/compile_madng.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 8e28696..3491434 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -172,11 +172,11 @@ jobs:
         ln -s lpeg-1.1.0 lpeg
         cd lpeg
         # Apply README.lpeg edits.
-        sed -i.bak \
-          -e 's#^#\\?LUADIR[[:space:]]*=.*#LUADIR = ../luajit/include/luajit-2.1#g' \
+        sed -i.bak -E \
+          -e 's#^#?LUADIR[[:space:]]*=.*#LUADIR = ../luajit/include/luajit-2.1#g' \
           -e 's#^LUALIB[[:space:]]*=.*#LUALIB = ../luajit/lib/libluajit-5.1.a#g' \
           -e 's#^COPT[[:space:]]*=.*#COPT = -O3 -DNDEBUG#g' \
-          makefile || true
+          makefile
         rm -f makefile.bak || true
         make clean || true
         make macosx

From 1d2028a4bca8377710201b446090377bb0dd4f4f Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 14:08:48 +0200
Subject: [PATCH 58/69] Update macOS build configuration and refine Makefile
 edits

---
 .github/workflows/compile_madng.yml | 129 +++++++++++-----------------
 1 file changed, 51 insertions(+), 78 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 3491434..f20a027 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -72,7 +72,7 @@ jobs:
         path: MAD/src/mad
 
   build-macos-arm:
-    runs-on: macos-latest
+    runs-on: macos-14
     defaults:
       run:
         shell: bash
@@ -91,72 +91,54 @@ jobs:
     - name: Install dependencies
       run: |
         brew update
-        # Pin GCC major to avoid runner drift.
         brew install gcc@13 make cmake automake libtool pkg-config
 
     - name: Select Makefile
       run: |
         cp MAD/src/Makefile.macosx MAD/src/Makefile
-        sed -i.bak \
-          -e "s#^CC[[:space:]]*:=.*#CC       := gcc#g" \
-          -e "s#^CXX[[:space:]]*:=.*#CXX      := g++#g" \
-          -e "s#^FC[[:space:]]*:=.*#FC       := gfortran#g" \
-          -e "s#-fdiagnostics-all-candidates##g" \
-          -e "s#-flto##g" \
-          -e "s#-march=native##g" \
-          -e "s#-mtune=native##g" \
-          -e "s#-mfma##g" \
+        sed -i.bak -E \
+          -e 's#^CC[[:space:]]*[:?]?=.*#CC = gcc#g' \
+          -e 's#^CXX[[:space:]]*[:?]?=.*#CXX = g++#g' \
+          -e 's#^FC[[:space:]]*[:?]?=.*#FC = gfortran#g' \
+          -e 's#-fdiagnostics-all-candidates##g' \
+          -e 's#-flto##g' \
+          -e 's#-march=native##g' \
+          -e 's#-mtune=native##g' \
+          -e 's#-mfma##g' \
           MAD/src/Makefile
 
-    - name: Build MAD-NG dependencies (README order)
+    - name: Build MAD-NG dependencies
       run: |
         set -euo pipefail
 
         gcc_prefix="$(brew --prefix gcc@13)"
-        gcc_bin="${gcc_prefix}/bin/gcc-13"
-        gxx_bin="${gcc_prefix}/bin/g++-13"
-        gfortran_bin="${gcc_prefix}/bin/gfortran-13"
-        test -x "${gcc_bin}" && test -x "${gxx_bin}" && test -x "${gfortran_bin}"
-
         toolshim="${RUNNER_TEMP}/gcc-shim"
         mkdir -p "${toolshim}"
-        ln -sf "${gcc_bin}" "${toolshim}/gcc"
-        ln -sf "${gxx_bin}" "${toolshim}/g++"
-        ln -sf "${gfortran_bin}" "${toolshim}/gfortran"
-        export PATH="${toolshim}:$(brew --prefix)/bin:${PATH}"
 
-        echo "== Toolchain =="
-        which gcc
-        gcc --version
-        which g++
-        g++ --version
-        which gfortran
-        gfortran --version
+        ln -sf "${gcc_prefix}/bin/gcc-13" "${toolshim}/gcc"
+        ln -sf "${gcc_prefix}/bin/g++-13" "${toolshim}/g++"
+        ln -sf "${gcc_prefix}/bin/gfortran-13" "${toolshim}/gfortran"
 
+        export PATH="${toolshim}:$(brew --prefix)/bin:${PATH}"
         export OS=macosx
         export MACOSX_DEPLOYMENT_TARGET=11
         export JOBS="$(sysctl -n hw.ncpu)"
 
         mkdir -p MAD/bin/macosx
-
-        # MAD-NG repo vendors third-party deps under MAD/lib (checked out with submodules).
         cd MAD/lib
-        echo "== MAD/lib contents =="
-        ls -la
 
-        echo "== LuaJIT (README.luajit) =="
+        echo "== LuaJIT =="
         rm -rf luajit
         git clone https://github.com/MethodicalAcceleratorDesign/LuaJIT.git luajit
         cd luajit
         git checkout mad-patch
-        git pull
-        make clean
+        make clean || true
         make -j"${JOBS}" amalg PREFIX="$(pwd)"
         make install PREFIX="$(pwd)"
         cp -f src/libluajit.a ../../bin/macosx/
         cd ..
 
-        echo "== LFS (README.lfs) =="
+        echo "== LFS =="
         rm -rf lfs
         git clone https://github.com/MethodicalAcceleratorDesign/luafilesystem.git lfs
         cd lfs
@@ -165,44 +147,40 @@ jobs:
         cp -f liblfs.a ../../bin/macosx/
         cd ..
 
-        echo "== LPEG (README.lpeg) =="
+        echo "== LPEG =="
         rm -rf lpeg lpeg-1.1.0 lpeg-1.1.0.tar.gz
-        curl -fsSL -o lpeg-1.1.0.tar.gz http://www.inf.puc-rio.br/~roberto/lpeg/lpeg-1.1.0.tar.gz
+        curl -fsSL -o lpeg-1.1.0.tar.gz https://www.inf.puc-rio.br/~roberto/lpeg/lpeg-1.1.0.tar.gz
         tar xvzf lpeg-1.1.0.tar.gz
         ln -s lpeg-1.1.0 lpeg
         cd lpeg
-        # Apply README.lpeg edits.
         sed -i.bak -E \
-          -e 's#^#?LUADIR[[:space:]]*=.*#LUADIR = ../luajit/include/luajit-2.1#g' \
+          -e 's#^LUADIR[[:space:]]*=.*#LUADIR = ../luajit/include/luajit-2.1#g' \
           -e 's#^LUALIB[[:space:]]*=.*#LUALIB = ../luajit/lib/libluajit-5.1.a#g' \
           -e 's#^COPT[[:space:]]*=.*#COPT = -O3 -DNDEBUG#g' \
           makefile
-        rm -f makefile.bak || true
         make clean || true
         make macosx
         cp -f liblpeg.a ../../bin/macosx/
         cd ..
 
-        echo "== LAPACK (README.lapack) =="
+        echo "== LAPACK =="
         rm -rf lapack
         git clone https://github.com/Reference-LAPACK/lapack lapack
         cd lapack
         cp -f make.inc.example make.inc
-        # Apply README.lapack edits: add -fPIC to CFLAGS/FFLAGS/FFLAGS_NOOPT.
         sed -i.bak -E \
-          -e 's#^(CFLAGS[[:space:]]*=[[:space:]]*)#\\1-fPIC #g' \
-          -e 's#^(FFLAGS[[:space:]]*=[[:space:]]*)#\\1-fPIC #g' \
-          -e 's#^(FFLAGS_NOOPT[[:space:]]*=[[:space:]]*)#\\1-fPIC #g' \
-          make.inc || true
-        rm -f make.inc.bak || true
+          -e 's#^(CFLAGS[[:space:]]*=[[:space:]]*)#\1-fPIC #g' \
+          -e 's#^(FFLAGS[[:space:]]*=[[:space:]]*)#\1-fPIC #g' \
+          -e 's#^(FFLAGS_NOOPT[[:space:]]*=[[:space:]]*)#\1-fPIC #g' \
+          make.inc
         make clean || true
         make -j"${JOBS}" lib
         cp -f liblapack.a librefblas.a ../../bin/macosx/
         cd ..
 
-        echo "== FFTW3 (README.fftw3) =="
+        echo "== FFTW3 =="
         rm -rf fftw3 fftw-3.3.10 fftw-3.3.10.tar.gz
-        curl -fsSL -o fftw-3.3.10.tar.gz ftp://ftp.fftw.org/pub/fftw/fftw-3.3.10.tar.gz
+        curl -fsSL -o fftw-3.3.10.tar.gz https://www.fftw.org/fftw-3.3.10.tar.gz
         tar xvzf fftw-3.3.10.tar.gz
         ln -s fftw-3.3.10 fftw3
         cd fftw3
@@ -212,60 +190,55 @@ jobs:
         cp -f .libs/libfftw3.a ../../bin/macosx/
         cd ..
 
-        echo "== NFFT3 (README.nfft3) =="
+        echo "== NFFT3 =="
         rm -rf nfft3 nfft-3.5.3 nfft-3.5.3.tar.gz
-        # README.nfft3 points to nfft.org; the upstream host also serves the tarball from TU Chemnitz.
         curl -fsSL -o nfft-3.5.3.tar.gz https://www-user.tu-chemnitz.de/~potts/nfft/download/nfft-3.5.3.tar.gz
         tar xvzf nfft-3.5.3.tar.gz
         ln -s nfft-3.5.3 nfft3
         cd nfft3
         make clean || true
         ./configure --enable-all --disable-shared \
-          --with-fftw3="$(pwd)"/../fftw3 \
-          --with-fftw3-libdir="$(pwd)"/../fftw3/.libs \
-          --with-fftw3-includedir="$(pwd)"/../fftw3/api
+          --with-fftw3="$(pwd)/../fftw3" \
+          --with-fftw3-libdir="$(pwd)/../fftw3/.libs" \
+          --with-fftw3-includedir="$(pwd)/../fftw3/api"
         make -j"${JOBS}"
         cp -f .libs/libnfft3.a ../../bin/macosx/
         cd ..
 
-        echo "== NLOPT (README.nlopt) =="
+        echo "== NLOPT =="
         rm -rf nlopt
         git clone https://github.com/stevengj/nlopt nlopt
         cd nlopt
-        rm -rf build
-        mkdir -p build
-        cd build
-        cmake -DBUILD_SHARED_LIBS=OFF -DNLOPT_CXX=OFF ..
-        make -j"${JOBS}"
-        cp -f libnlopt.a ../../../bin/macosx/
-        cd ../..
+        cmake -S . -B build \
+          -DBUILD_SHARED_LIBS=OFF \
+          -DNLOPT_CXX=OFF
+        cmake --build build --parallel "${JOBS}"
+        cp -f build/libnlopt.a ../../bin/macosx/
 
     - name: Compile MAD-NG
       working-directory: MAD/src
       run: |
+        set -euo pipefail
+
         gcc_prefix="$(brew --prefix gcc@13)"
-        gcc_bin="${gcc_prefix}/bin/gcc-13"
-        gxx_bin="${gcc_prefix}/bin/g++-13"
-        gfortran_bin="${gcc_prefix}/bin/gfortran-13"
-        test -x "${gcc_bin}" && test -x "${gxx_bin}" && test -x "${gfortran_bin}"
         toolshim="${RUNNER_TEMP}/gcc-shim"
         mkdir -p "${toolshim}"
-        ln -sf "${gcc_bin}" "${toolshim}/gcc"
-        ln -sf "${gxx_bin}" "${toolshim}/g++"
-        ln -sf "${gfortran_bin}" "${toolshim}/gfortran"
+
+        ln -sf "${gcc_prefix}/bin/gcc-13" "${toolshim}/gcc"
+        ln -sf "${gcc_prefix}/bin/g++-13" "${toolshim}/g++"
+        ln -sf "${gcc_prefix}/bin/gfortran-13" "${toolshim}/gfortran"
+
         export PATH="${toolshim}:$(brew --prefix)/bin:${PATH}"
+        export MACOSX_DEPLOYMENT_TARGET=11
 
-        echo "== Toolchain =="
-        which gcc
-        gcc --version
-        which g++
-        g++ --version
-        which gfortran
-        gfortran --version
         make SHELL=/bin/bash CC=gcc CXX=g++ FC=gfortran
 
+        chmod 755 mad
+        file mad
+        ./mad -v || ./mad --version || true
+
     - name: Upload binary
       uses: actions/upload-artifact@v4
       with:
         name: mad-macOS-ARM
-        path: MAD/src/mad
+        path: MAD/src/mad
\ No newline at end of file

From 40b78ecfae86cdb30257d75ffa0e27545ad11582 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 14:24:02 +0200
Subject: [PATCH 59/69] Enhance macOS build workflow for arm64 architecture and
 update dependencies

---
 .github/workflows/compile_madng.yml | 130 +++++++++++++++-------------
 1 file changed, 72 insertions(+), 58 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index f20a027..460f1db 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -71,7 +71,7 @@ jobs:
         name: mad-Linux
         path: MAD/src/mad
 
-  build-macos-arm:
+  build-macos-arm64:
     runs-on: macos-14
     defaults:
       run:
@@ -88,26 +88,12 @@ jobs:
         path: MAD
         submodules: recursive
 
-    - name: Install dependencies
+    - name: Install build tools
       run: |
         brew update
-        brew install gcc@13 make cmake automake libtool pkg-config
+        brew install gcc@13 make cmake automake autoconf libtool pkg-config curl
 
-    - name: Select Makefile
-      run: |
-        cp MAD/src/Makefile.macosx MAD/src/Makefile
-        sed -i.bak -E \
-          -e 's#^CC[[:space:]]*[:?]?=.*#CC = gcc#g' \
-          -e 's#^CXX[[:space:]]*[:?]?=.*#CXX = g++#g' \
-          -e 's#^FC[[:space:]]*[:?]?=.*#FC = gfortran#g' \
-          -e 's#-fdiagnostics-all-candidates##g' \
-          -e 's#-flto##g' \
-          -e 's#-march=native##g' \
-          -e 's#-mtune=native##g' \
-          -e 's#-mfma##g' \
-          MAD/src/Makefile
-
-    - name: Build MAD-NG dependencies
+    - name: Prepare compiler shims
       run: |
         set -euo pipefail
 
@@ -119,26 +105,60 @@ jobs:
         ln -sf "${gcc_prefix}/bin/g++-13" "${toolshim}/g++"
         ln -sf "${gcc_prefix}/bin/gfortran-13" "${toolshim}/gfortran"
 
-        export PATH="${toolshim}:$(brew --prefix)/bin:${PATH}"
+        {
+          echo "${toolshim}"
+          echo "$(brew --prefix)/bin"
+        } >> "${GITHUB_PATH}"
+
+    - name: Select MAD-NG macOS Makefile
+      run: |
+        cp MAD/src/Makefile.macosx MAD/src/Makefile
+        sed -i.bak \
+          -e "s#^CC[[:space:]]*:=.*#CC       := gcc#g" \
+          -e "s#^CXX[[:space:]]*:=.*#CXX      := g++#g" \
+          -e "s#^FC[[:space:]]*:=.*#FC       := gfortran#g" \
+          -e "s#-fdiagnostics-all-candidates##g" \
+          -e "s#-flto##g" \
+          -e "s#-march=native##g" \
+          -e "s#-mtune=native##g" \
+          -e "s#-mfma##g" \
+          MAD/src/Makefile
+
+    - name: Build MAD-NG dependencies (README order)
+      run: |
+        set -euo pipefail
+
+        echo "== Toolchain =="
+        which gcc
+        gcc --version
+        which g++
+        g++ --version
+        which gfortran
+        gfortran --version
+
         export OS=macosx
         export MACOSX_DEPLOYMENT_TARGET=11
         export JOBS="$(sysctl -n hw.ncpu)"
 
         mkdir -p MAD/bin/macosx
+
         cd MAD/lib
+        echo "== MAD/lib contents (before download) =="
+        ls -la
 
-        echo "== LuaJIT =="
+        echo "== LuaJIT (README.luajit) =="
         rm -rf luajit
         git clone https://github.com/MethodicalAcceleratorDesign/LuaJIT.git luajit
         cd luajit
         git checkout mad-patch
-        make clean || true
+        git pull
+        make clean
         make -j"${JOBS}" amalg PREFIX="$(pwd)"
         make install PREFIX="$(pwd)"
         cp -f src/libluajit.a ../../bin/macosx/
         cd ..
 
-        echo "== LFS =="
+        echo "== LFS (README.lfs) =="
         rm -rf lfs
         git clone https://github.com/MethodicalAcceleratorDesign/luafilesystem.git lfs
         cd lfs
@@ -147,40 +167,42 @@ jobs:
         cp -f liblfs.a ../../bin/macosx/
         cd ..
 
-        echo "== LPEG =="
+        echo "== LPEG (README.lpeg) =="
         rm -rf lpeg lpeg-1.1.0 lpeg-1.1.0.tar.gz
-        curl -fsSL -o lpeg-1.1.0.tar.gz https://www.inf.puc-rio.br/~roberto/lpeg/lpeg-1.1.0.tar.gz
+        curl -fsSL -o lpeg-1.1.0.tar.gz http://www.inf.puc-rio.br/~roberto/lpeg/lpeg-1.1.0.tar.gz
         tar xvzf lpeg-1.1.0.tar.gz
         ln -s lpeg-1.1.0 lpeg
         cd lpeg
         sed -i.bak -E \
-          -e 's#^LUADIR[[:space:]]*=.*#LUADIR = ../luajit/include/luajit-2.1#g' \
+          -e 's#^#?LUADIR[[:space:]]*=.*#LUADIR = ../luajit/include/luajit-2.1#g' \
           -e 's#^LUALIB[[:space:]]*=.*#LUALIB = ../luajit/lib/libluajit-5.1.a#g' \
           -e 's#^COPT[[:space:]]*=.*#COPT = -O3 -DNDEBUG#g' \
           makefile
+        rm -f makefile.bak || true
         make clean || true
         make macosx
         cp -f liblpeg.a ../../bin/macosx/
         cd ..
 
-        echo "== LAPACK =="
+        echo "== LAPACK (README.lapack) =="
         rm -rf lapack
         git clone https://github.com/Reference-LAPACK/lapack lapack
         cd lapack
         cp -f make.inc.example make.inc
         sed -i.bak -E \
-          -e 's#^(CFLAGS[[:space:]]*=[[:space:]]*)#\1-fPIC #g' \
-          -e 's#^(FFLAGS[[:space:]]*=[[:space:]]*)#\1-fPIC #g' \
-          -e 's#^(FFLAGS_NOOPT[[:space:]]*=[[:space:]]*)#\1-fPIC #g' \
+          -e 's#^(CFLAGS[[:space:]]*=[[:space:]]*)#\\1-fPIC #g' \
+          -e 's#^(FFLAGS[[:space:]]*=[[:space:]]*)#\\1-fPIC #g' \
+          -e 's#^(FFLAGS_NOOPT[[:space:]]*=[[:space:]]*)#\\1-fPIC #g' \
           make.inc
+        rm -f make.inc.bak || true
         make clean || true
         make -j"${JOBS}" lib
         cp -f liblapack.a librefblas.a ../../bin/macosx/
         cd ..
 
-        echo "== FFTW3 =="
+        echo "== FFTW3 (README.fftw3) =="
         rm -rf fftw3 fftw-3.3.10 fftw-3.3.10.tar.gz
-        curl -fsSL -o fftw-3.3.10.tar.gz https://www.fftw.org/fftw-3.3.10.tar.gz
+        curl -fsSL -o fftw-3.3.10.tar.gz ftp://ftp.fftw.org/pub/fftw/fftw-3.3.10.tar.gz
         tar xvzf fftw-3.3.10.tar.gz
         ln -s fftw-3.3.10 fftw3
         cd fftw3
@@ -190,7 +212,7 @@ jobs:
         cp -f .libs/libfftw3.a ../../bin/macosx/
         cd ..
 
-        echo "== NFFT3 =="
+        echo "== NFFT3 (README.nfft3) =="
         rm -rf nfft3 nfft-3.5.3 nfft-3.5.3.tar.gz
         curl -fsSL -o nfft-3.5.3.tar.gz https://www-user.tu-chemnitz.de/~potts/nfft/download/nfft-3.5.3.tar.gz
         tar xvzf nfft-3.5.3.tar.gz
@@ -198,47 +220,39 @@ jobs:
         cd nfft3
         make clean || true
         ./configure --enable-all --disable-shared \
-          --with-fftw3="$(pwd)/../fftw3" \
-          --with-fftw3-libdir="$(pwd)/../fftw3/.libs" \
-          --with-fftw3-includedir="$(pwd)/../fftw3/api"
+          --with-fftw3="$(pwd)"/../fftw3 \
+          --with-fftw3-libdir="$(pwd)"/../fftw3/.libs \
+          --with-fftw3-includedir="$(pwd)"/../fftw3/api
         make -j"${JOBS}"
         cp -f .libs/libnfft3.a ../../bin/macosx/
         cd ..
 
-        echo "== NLOPT =="
+        echo "== NLOPT (README.nlopt) =="
         rm -rf nlopt
         git clone https://github.com/stevengj/nlopt nlopt
         cd nlopt
-        cmake -S . -B build \
-          -DBUILD_SHARED_LIBS=OFF \
-          -DNLOPT_CXX=OFF
-        cmake --build build --parallel "${JOBS}"
-        cp -f build/libnlopt.a ../../bin/macosx/
+        rm -rf build
+        mkdir -p build
+        cd build
+        cmake -DBUILD_SHARED_LIBS=OFF -DNLOPT_CXX=OFF ..
+        make -j"${JOBS}"
+        cp -f libnlopt.a ../../../bin/macosx/
 
     - name: Compile MAD-NG
       working-directory: MAD/src
       run: |
-        set -euo pipefail
-
-        gcc_prefix="$(brew --prefix gcc@13)"
-        toolshim="${RUNNER_TEMP}/gcc-shim"
-        mkdir -p "${toolshim}"
-
-        ln -sf "${gcc_prefix}/bin/gcc-13" "${toolshim}/gcc"
-        ln -sf "${gcc_prefix}/bin/g++-13" "${toolshim}/g++"
-        ln -sf "${gcc_prefix}/bin/gfortran-13" "${toolshim}/gfortran"
-
-        export PATH="${toolshim}:$(brew --prefix)/bin:${PATH}"
-        export MACOSX_DEPLOYMENT_TARGET=11
+        echo "== Toolchain =="
+        which gcc
+        gcc --version
+        which g++
+        g++ --version
+        which gfortran
+        gfortran --version
 
         make SHELL=/bin/bash CC=gcc CXX=g++ FC=gfortran
 
-        chmod 755 mad
-        file mad
-        ./mad -v || ./mad --version || true
-
     - name: Upload binary
       uses: actions/upload-artifact@v4
       with:
         name: mad-macOS-ARM
-        path: MAD/src/mad
\ No newline at end of file
+        path: MAD/src/mad

From 0347b2da9e3f95ca0b82e035501b928334f86e91 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 14:31:15 +0200
Subject: [PATCH 60/69] Refactor Makefile modifications to use Python for
 replacements in macOS build process

---
 .github/workflows/compile_madng.yml | 59 ++++++++++++++++++-----------
 1 file changed, 37 insertions(+), 22 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 460f1db..7f37743 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -113,16 +113,24 @@ jobs:
     - name: Select MAD-NG macOS Makefile
       run: |
         cp MAD/src/Makefile.macosx MAD/src/Makefile
-        sed -i.bak \
-          -e "s#^CC[[:space:]]*:=.*#CC       := gcc#g" \
-          -e "s#^CXX[[:space:]]*:=.*#CXX      := g++#g" \
-          -e "s#^FC[[:space:]]*:=.*#FC       := gfortran#g" \
-          -e "s#-fdiagnostics-all-candidates##g" \
-          -e "s#-flto##g" \
-          -e "s#-march=native##g" \
-          -e "s#-mtune=native##g" \
-          -e "s#-mfma##g" \
-          MAD/src/Makefile
+        python3 - <<'PY'
+        from pathlib import Path
+        path = Path("MAD/src/Makefile")
+        text = path.read_text()
+        replacements = [
+            ("CC       := gcc-11", "CC       := gcc"),
+            ("CXX      := g++-11", "CXX      := g++"),
+            ("FC       := gfortran-11", "FC       := gfortran"),
+            ("-fdiagnostics-all-candidates", ""),
+            ("-flto", ""),
+            ("-march=native", ""),
+            ("-mtune=native", ""),
+            ("-mfma", ""),
+        ]
+        for old, new in replacements:
+            text = text.replace(old, new)
+        path.write_text(text)
+        PY
 
     - name: Build MAD-NG dependencies (README order)
       run: |
@@ -173,12 +181,16 @@ jobs:
         tar xvzf lpeg-1.1.0.tar.gz
         ln -s lpeg-1.1.0 lpeg
         cd lpeg
-        sed -i.bak -E \
-          -e 's#^#?LUADIR[[:space:]]*=.*#LUADIR = ../luajit/include/luajit-2.1#g' \
-          -e 's#^LUALIB[[:space:]]*=.*#LUALIB = ../luajit/lib/libluajit-5.1.a#g' \
-          -e 's#^COPT[[:space:]]*=.*#COPT = -O3 -DNDEBUG#g' \
-          makefile
-        rm -f makefile.bak || true
+        python3 - <<'PY'
+        from pathlib import Path
+        import re
+        path = Path("makefile")
+        text = path.read_text()
+        text = re.sub(r"^LUADIR[ \t]*=.*$", "LUADIR = ../luajit/include/luajit-2.1", text, flags=re.MULTILINE)
+        text = re.sub(r"^LUALIB[ \t]*=.*$", "LUALIB = ../luajit/lib/libluajit-5.1.a", text, flags=re.MULTILINE)
+        text = re.sub(r"^COPT[ \t]*=.*$", "COPT = -O3 -DNDEBUG", text, flags=re.MULTILINE)
+        path.write_text(text)
+        PY
         make clean || true
         make macosx
         cp -f liblpeg.a ../../bin/macosx/
@@ -189,12 +201,15 @@ jobs:
         git clone https://github.com/Reference-LAPACK/lapack lapack
         cd lapack
         cp -f make.inc.example make.inc
-        sed -i.bak -E \
-          -e 's#^(CFLAGS[[:space:]]*=[[:space:]]*)#\\1-fPIC #g' \
-          -e 's#^(FFLAGS[[:space:]]*=[[:space:]]*)#\\1-fPIC #g' \
-          -e 's#^(FFLAGS_NOOPT[[:space:]]*=[[:space:]]*)#\\1-fPIC #g' \
-          make.inc
-        rm -f make.inc.bak || true
+        python3 - <<'PY'
+        from pathlib import Path
+        import re
+        path = Path("make.inc")
+        text = path.read_text()
+        for key in ("CFLAGS", "FFLAGS", "FFLAGS_NOOPT"):
+            text = re.sub(rf"^({key}[ \t]*=[ \t]*)(?!-fPIC\b)", r"\1-fPIC ", text, flags=re.MULTILINE)
+        path.write_text(text)
+        PY
         make clean || true
         make -j"${JOBS}" lib
         cp -f liblapack.a librefblas.a ../../bin/macosx/

From ad678b33d141b324782628d7c416a31238feb0dd Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 14:35:43 +0200
Subject: [PATCH 61/69] on push

---
 .github/workflows/compile_madng.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 7f37743..527e230 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -1,8 +1,10 @@
 name: Make a MAD-NG Binary
 
 on:
+  push:
   workflow_dispatch:
 
+
 jobs:
   build-linux:
     runs-on: ubuntu-22.04
@@ -192,7 +194,9 @@ jobs:
         path.write_text(text)
         PY
         make clean || true
-        make macosx
+        make -j"${JOBS}" CC="${CC:-gcc}" LUADIR="../luajit/include/luajit-2.1" lpvm.o lpcap.o lptree.o lpcode.o lpprint.o lpcset.o
+        ar -r liblpeg.a lpvm.o lpcap.o lptree.o lpcode.o lpprint.o lpcset.o
+        ranlib liblpeg.a
         cp -f liblpeg.a ../../bin/macosx/
         cd ..
 

From cfb86c3f6677d4f0c50303af2a9ae59d7a650f77 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 14:44:01 +0200
Subject: [PATCH 62/69] more fixes

---
 .github/workflows/compile_madng.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 527e230..33416f6 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -215,8 +215,10 @@ jobs:
         path.write_text(text)
         PY
         make clean || true
-        make -j"${JOBS}" lib
-        cp -f liblapack.a librefblas.a ../../bin/macosx/
+        make -j"${JOBS}" blaslib
+        make -j"${JOBS}" lapacklib
+        cp -f librefblas.a ../../bin/macosx/
+        cp -f liblapack.a ../../bin/macosx/
         cd ..
 
         echo "== FFTW3 (README.fftw3) =="

From 627f8f9c1cd9d64d7bfd92b087aead8a76a76c30 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 14:54:11 +0200
Subject: [PATCH 63/69] Rename macOS build job to x86_64 and update toolchain
 to use gcc@12

---
 .github/workflows/compile_madng.yml | 35 +++++++++++++++++++++--------
 1 file changed, 26 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 33416f6..8dc66e7 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -73,7 +73,7 @@ jobs:
         name: mad-Linux
         path: MAD/src/mad
 
-  build-macos-arm64:
+  build-macos-x86_64:
     runs-on: macos-14
     defaults:
       run:
@@ -92,24 +92,31 @@ jobs:
 
     - name: Install build tools
       run: |
-        brew update
-        brew install gcc@13 make cmake automake autoconf libtool pkg-config curl
+        arch -x86_64 /usr/local/bin/brew update
+        arch -x86_64 /usr/local/bin/brew install gcc@12 make cmake automake autoconf libtool pkg-config curl
 
     - name: Prepare compiler shims
       run: |
         set -euo pipefail
 
-        gcc_prefix="$(brew --prefix gcc@13)"
+        gcc_prefix="$(arch -x86_64 /usr/local/bin/brew --prefix gcc@12)"
         toolshim="${RUNNER_TEMP}/gcc-shim"
         mkdir -p "${toolshim}"
 
-        ln -sf "${gcc_prefix}/bin/gcc-13" "${toolshim}/gcc"
-        ln -sf "${gcc_prefix}/bin/g++-13" "${toolshim}/g++"
-        ln -sf "${gcc_prefix}/bin/gfortran-13" "${toolshim}/gfortran"
+        ln -sf "${gcc_prefix}/bin/gcc-12" "${toolshim}/gcc"
+        ln -sf "${gcc_prefix}/bin/g++-12" "${toolshim}/g++"
+        ln -sf "${gcc_prefix}/bin/gfortran-12" "${toolshim}/gfortran"
+        ln -sf "/usr/local/bin/make" "${toolshim}/make"
+        ln -sf "/usr/local/bin/cmake" "${toolshim}/cmake"
+        ln -sf "/usr/local/bin/pkg-config" "${toolshim}/pkg-config"
+        ln -sf "/usr/local/bin/libtool" "${toolshim}/libtool"
+        ln -sf "/usr/local/bin/ar" "${toolshim}/ar"
+        ln -sf "/usr/local/bin/ranlib" "${toolshim}/ranlib"
 
         {
           echo "${toolshim}"
-          echo "$(brew --prefix)/bin"
+          echo "/usr/local/bin"
+          echo "$(arch -x86_64 /usr/local/bin/brew --prefix)/bin"
         } >> "${GITHUB_PATH}"
 
     - name: Select MAD-NG macOS Makefile
@@ -149,6 +156,16 @@ jobs:
         export OS=macosx
         export MACOSX_DEPLOYMENT_TARGET=11
         export JOBS="$(sysctl -n hw.ncpu)"
+        export CC=gcc
+        export CXX=g++
+        export FC=gfortran
+        export AR=ar
+        export RANLIB=ranlib
+        export CFLAGS="-arch x86_64"
+        export CXXFLAGS="-arch x86_64"
+        export FFLAGS="-arch x86_64"
+        export FCFLAGS="-arch x86_64"
+        export LDFLAGS="-arch x86_64"
 
         mkdir -p MAD/bin/macosx
 
@@ -275,5 +292,5 @@ jobs:
     - name: Upload binary
       uses: actions/upload-artifact@v4
       with:
-        name: mad-macOS-ARM
+        name: mad-macOS-x86_64
         path: MAD/src/mad

From e74c138ba433c9d626f2443658d515ff57739e1f Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 15:26:21 +0200
Subject: [PATCH 64/69] Update compile_madng.yml

---
 .github/workflows/compile_madng.yml | 179 +++++++++++++++++++++++++++-
 1 file changed, 175 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 8dc66e7..35a0b2f 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -74,7 +74,7 @@ jobs:
         path: MAD/src/mad
 
   build-macos-x86_64:
-    runs-on: macos-14
+    runs-on: macos-14-large
     defaults:
       run:
         shell: bash
@@ -92,20 +92,191 @@ jobs:
 
     - name: Install build tools
       run: |
-        arch -x86_64 /usr/local/bin/brew update
-        arch -x86_64 /usr/local/bin/brew install gcc@12 make cmake automake autoconf libtool pkg-config curl
+        brew update
+        brew install gcc@12 make cmake automake autoconf libtool pkg-config curl
 
     - name: Prepare compiler shims
       run: |
         set -euo pipefail
 
-        gcc_prefix="$(arch -x86_64 /usr/local/bin/brew --prefix gcc@12)"
+        gcc_prefix="$(brew --prefix gcc@12)"
         toolshim="${RUNNER_TEMP}/gcc-shim"
         mkdir -p "${toolshim}"
 
         ln -sf "${gcc_prefix}/bin/gcc-12" "${toolshim}/gcc"
         ln -sf "${gcc_prefix}/bin/g++-12" "${toolshim}/g++"
         ln -sf "${gcc_prefix}/bin/gfortran-12" "${toolshim}/gfortran"
+
+        {
+          echo "${toolshim}"
+          echo "$(brew --prefix)/bin"
+        } >> "${GITHUB_PATH}"
+
+    - name: Select MAD-NG macOS Makefile
+      run: |
+        cp MAD/src/Makefile.macosx MAD/src/Makefile
+        python3 - <<'PY'
+        from pathlib import Path
+
+        path = Path("MAD/src/Makefile")
+        text = path.read_text()
+
+        replacements = [
+            ("CC       := gcc-11", "CC       := gcc"),
+            ("CXX      := g++-11", "CXX      := g++"),
+            ("FC       := gfortran-11", "FC       := gfortran"),
+            ("-fdiagnostics-all-candidates", ""),
+            ("-flto", ""),
+            ("-march=native", ""),
+            ("-mtune=native", ""),
+            ("-mfma", ""),
+        ]
+
+        for old, new in replacements:
+            text = text.replace(old, new)
+
+        path.write_text(text)
+        PY
+
+    - name: Build MAD-NG dependencies
+      run: |
+        set -euo pipefail
+
+        export OS=macosx
+        export MACOSX_DEPLOYMENT_TARGET=11
+        export JOBS="$(sysctl -n hw.ncpu)"
+        export CC=gcc
+        export CXX=g++
+        export FC=gfortran
+        export AR=ar
+        export RANLIB=ranlib
+
+        mkdir -p MAD/tools
+        cp -f tools/build_madng_deps_linux.sh MAD/tools/ || true
+
+        mkdir -p MAD/bin/macosx
+
+        cd MAD/lib
+
+        rm -rf luajit
+        git clone https://github.com/MethodicalAcceleratorDesign/LuaJIT.git luajit
+        cd luajit
+        git checkout mad-patch
+        make clean || true
+        make -j"${JOBS}" amalg PREFIX="$(pwd)"
+        make install PREFIX="$(pwd)"
+        cp -f src/libluajit.a ../../bin/macosx/
+        cd ..
+
+        rm -rf lfs
+        git clone https://github.com/MethodicalAcceleratorDesign/luafilesystem.git lfs
+        cd lfs
+        make clean || true
+        make lfs.a
+        cp -f liblfs.a ../../bin/macosx/
+        cd ..
+
+        rm -rf lpeg lpeg-1.1.0 lpeg-1.1.0.tar.gz
+        curl -fsSL -o lpeg-1.1.0.tar.gz http://www.inf.puc-rio.br/~roberto/lpeg/lpeg-1.1.0.tar.gz
+        tar xzf lpeg-1.1.0.tar.gz
+        ln -s lpeg-1.1.0 lpeg
+        cd lpeg
+        python3 - <<'PY'
+        from pathlib import Path
+        import re
+
+        path = Path("makefile")
+        text = path.read_text()
+        text = re.sub(r"^LUADIR[ \t]*=.*$", "LUADIR = ../luajit/include/luajit-2.1", text, flags=re.MULTILINE)
+        text = re.sub(r"^LUALIB[ \t]*=.*$", "LUALIB = ../luajit/lib/libluajit-5.1.a", text, flags=re.MULTILINE)
+        text = re.sub(r"^COPT[ \t]*=.*$", "COPT = -O3 -DNDEBUG", text, flags=re.MULTILINE)
+        path.write_text(text)
+        PY
+        make clean || true
+        make -j"${JOBS}" CC=gcc LUADIR="../luajit/include/luajit-2.1" \
+          lpvm.o lpcap.o lptree.o lpcode.o lpprint.o lpcset.o
+        ar -r liblpeg.a lpvm.o lpcap.o lptree.o lpcode.o lpprint.o lpcset.o
+        ranlib liblpeg.a
+        cp -f liblpeg.a ../../bin/macosx/
+        cd ..
+
+        rm -rf lapack
+        git clone https://github.com/Reference-LAPACK/lapack lapack
+        cd lapack
+        cp -f make.inc.example make.inc
+        python3 - <<'PY'
+        from pathlib import Path
+        import re
+
+        path = Path("make.inc")
+        text = path.read_text()
+        for key in ("CFLAGS", "FFLAGS", "FFLAGS_NOOPT"):
+            text = re.sub(rf"^({key}[ \t]*=[ \t]*)(?!-fPIC\b)", r"\1-fPIC ", text, flags=re.MULTILINE)
+        path.write_text(text)
+        PY
+        make clean || true
+        make -j"${JOBS}" blaslib
+        make -j"${JOBS}" lapacklib
+        cp -f librefblas.a ../../bin/macosx/
+        cp -f liblapack.a ../../bin/macosx/
+        cd ..
+
+        rm -rf fftw3 fftw-3.3.10 fftw-3.3.10.tar.gz
+        curl -fsSL -o fftw-3.3.10.tar.gz https://www.fftw.org/fftw-3.3.10.tar.gz
+        tar xzf fftw-3.3.10.tar.gz
+        ln -s fftw-3.3.10 fftw3
+        cd fftw3
+        make clean || true
+        ./configure --disable-shared
+        make -j"${JOBS}"
+        cp -f .libs/libfftw3.a ../../bin/macosx/
+        cd ..
+
+        rm -rf nfft3 nfft-3.5.3 nfft-3.5.3.tar.gz
+        curl -fsSL -o nfft-3.5.3.tar.gz https://www-user.tu-chemnitz.de/~potts/nfft/download/nfft-3.5.3.tar.gz
+        tar xzf nfft-3.5.3.tar.gz
+        ln -s nfft-3.5.3 nfft3
+        cd nfft3
+        make clean || true
+        ./configure --enable-all --disable-shared \
+          --with-fftw3="$(pwd)/../fftw3" \
+          --with-fftw3-libdir="$(pwd)/../fftw3/.libs" \
+          --with-fftw3-includedir="$(pwd)/../fftw3/api"
+        make -j"${JOBS}"
+        cp -f .libs/libnfft3.a ../../bin/macosx/
+        cd ..
+
+        rm -rf nlopt
+        git clone https://github.com/stevengj/nlopt nlopt
+        cd nlopt
+        mkdir -p build
+        cd build
+        cmake -DBUILD_SHARED_LIBS=OFF -DNLOPT_CXX=OFF ..
+        make -j"${JOBS}"
+        cp -f libnlopt.a ../../../bin/macosx/
+
+    - name: Compile MAD-NG
+      working-directory: MAD/src
+      run: |
+        set -euo pipefail
+
+        which gcc
+        gcc --version
+        which g++
+        g++ --version
+        which gfortran
+        gfortran --version
+
+        make SHELL=/bin/bash CC=gcc CXX=g++ FC=gfortran
+
+        file mad
+        otool -L mad || true
+
+    - name: Upload binary
+      uses: actions/upload-artifact@v4
+      with:
+        name: mad-macOS-x86_64
+        path: MAD/src/mad
         ln -sf "/usr/local/bin/make" "${toolshim}/make"
         ln -sf "/usr/local/bin/cmake" "${toolshim}/cmake"
         ln -sf "/usr/local/bin/pkg-config" "${toolshim}/pkg-config"

From a7b77036605d09b1681f16bfd7d29572802acb6d Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 15:29:09 +0200
Subject: [PATCH 65/69] Update compile_madng.yml

---
 .github/workflows/compile_madng.yml | 715 +++++++++++-----------------
 1 file changed, 270 insertions(+), 445 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 35a0b2f..6be78ad 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -4,7 +4,6 @@ on:
   push:
   workflow_dispatch:
 
-
 jobs:
   build-linux:
     runs-on: ubuntu-22.04
@@ -13,65 +12,63 @@ jobs:
         shell: bash
 
     steps:
-    - name: Checkout current repo
-      uses: actions/checkout@v4
-
-    - name: Clone MAD-NG
-      uses: actions/checkout@v4
-      with:
-        repository: MethodicalAcceleratorDesign/MAD-NG
-        path: MAD
-        submodules: recursive
-
-    - name: Build MAD-NG in Rocky Linux 9
-      run: |
-        docker run --rm \
-          -v "${GITHUB_WORKSPACE}:/work" \
-          -w /work \
-          rockylinux:9 \
-          bash -lc '
-            set -euo pipefail
-
-            dnf install -y dnf-plugins-core
-            dnf config-manager --enable crb
-            dnf install -y \
-              gcc gcc-c++ gcc-gfortran make cmake git \
-              libquadmath-devel libquadmath-static \
-              libgfortran-static libstdc++-static \
-              diffutils findutils sed which tar gzip
-
-            cp MAD/src/Makefile.lxplus MAD/src/Makefile
-            sed -i \
-              -e '"'"'s#^CC[[:space:]]*=.*#CC=gcc#g'"'"' \
-              -e '"'"'s#^CXX[[:space:]]*=.*#CXX=g++#g'"'"' \
-              -e '"'"'s#-fdiagnostics-all-candidates##g'"'"' \
-              MAD/src/Makefile || true
-
-            mkdir -p MAD/tools
-            cp -f tools/build_madng_deps_linux.sh MAD/tools/
-            chmod +x MAD/tools/build_madng_deps_linux.sh
-            (cd MAD && JOBS="$(nproc)" CC=gcc CXX=g++ FC=gfortran AR=ar RANLIB=ranlib ./tools/build_madng_deps_linux.sh)
-
-            cd MAD/src
-            export CC=gcc CXX=g++
-            # LIBRARY_PATH makes GCC prepend -L at the START of the ld invocation,
-            # before -lgfortran/-lquadmath are seen (unlike LDOPTIONS which comes after).
-            gcc_libdir="$(gcc -print-libgcc-file-name | xargs dirname)"
-            export LIBRARY_PATH="${gcc_libdir}${LIBRARY_PATH:+:${LIBRARY_PATH}}"
-            export LDOPTIONS="-no-pie"
-
-            make SHELL=/bin/bash \
-              CC="${CC}" CXX="${CXX}" \
-              LDOPTIONS="${LDOPTIONS:-}"
-
-            chmod 755 mad
-          '
-
-    - name: Upload binary
-      uses: actions/upload-artifact@v4
-      with:
-        name: mad-Linux
-        path: MAD/src/mad
+      - name: Checkout current repo
+        uses: actions/checkout@v4
+
+      - name: Clone MAD-NG
+        uses: actions/checkout@v4
+        with:
+          repository: MethodicalAcceleratorDesign/MAD-NG
+          path: MAD
+          submodules: recursive
+
+      - name: Build MAD-NG in Rocky Linux 9
+        run: |
+          docker run --rm \
+            -v "${GITHUB_WORKSPACE}:/work" \
+            -w /work \
+            rockylinux:9 \
+            bash -lc '
+              set -euo pipefail
+
+              dnf install -y dnf-plugins-core
+              dnf config-manager --enable crb
+              dnf install -y \
+                gcc gcc-c++ gcc-gfortran make cmake git \
+                libquadmath-devel libquadmath-static \
+                libgfortran-static libstdc++-static \
+                diffutils findutils sed which tar gzip
+
+              cp MAD/src/Makefile.lxplus MAD/src/Makefile
+              sed -i \
+                -e '"'"'s#^CC[[:space:]]*=.*#CC=gcc#g'"'"' \
+                -e '"'"'s#^CXX[[:space:]]*=.*#CXX=g++#g'"'"' \
+                -e '"'"'s#-fdiagnostics-all-candidates##g'"'"' \
+                MAD/src/Makefile || true
+
+              mkdir -p MAD/tools
+              cp -f tools/build_madng_deps_linux.sh MAD/tools/
+              chmod +x MAD/tools/build_madng_deps_linux.sh
+              (cd MAD && JOBS="$(nproc)" CC=gcc CXX=g++ FC=gfortran AR=ar RANLIB=ranlib ./tools/build_madng_deps_linux.sh)
+
+              cd MAD/src
+              export CC=gcc CXX=g++
+              gcc_libdir="$(gcc -print-libgcc-file-name | xargs dirname)"
+              export LIBRARY_PATH="${gcc_libdir}${LIBRARY_PATH:+:${LIBRARY_PATH}}"
+              export LDOPTIONS="-no-pie"
+
+              make SHELL=/bin/bash \
+                CC="${CC}" CXX="${CXX}" \
+                LDOPTIONS="${LDOPTIONS:-}"
+
+              chmod 755 mad
+            '
+
+      - name: Upload binary
+        uses: actions/upload-artifact@v4
+        with:
+          name: mad-Linux
+          path: MAD/src/mad
 
   build-macos-x86_64:
     runs-on: macos-14-large
@@ -80,388 +77,216 @@ jobs:
         shell: bash
 
     steps:
-    - name: Checkout current repo
-      uses: actions/checkout@v4
-
-    - name: Clone MAD-NG
-      uses: actions/checkout@v4
-      with:
-        repository: MethodicalAcceleratorDesign/MAD-NG
-        path: MAD
-        submodules: recursive
-
-    - name: Install build tools
-      run: |
-        brew update
-        brew install gcc@12 make cmake automake autoconf libtool pkg-config curl
-
-    - name: Prepare compiler shims
-      run: |
-        set -euo pipefail
-
-        gcc_prefix="$(brew --prefix gcc@12)"
-        toolshim="${RUNNER_TEMP}/gcc-shim"
-        mkdir -p "${toolshim}"
-
-        ln -sf "${gcc_prefix}/bin/gcc-12" "${toolshim}/gcc"
-        ln -sf "${gcc_prefix}/bin/g++-12" "${toolshim}/g++"
-        ln -sf "${gcc_prefix}/bin/gfortran-12" "${toolshim}/gfortran"
-
-        {
-          echo "${toolshim}"
-          echo "$(brew --prefix)/bin"
-        } >> "${GITHUB_PATH}"
-
-    - name: Select MAD-NG macOS Makefile
-      run: |
-        cp MAD/src/Makefile.macosx MAD/src/Makefile
-        python3 - <<'PY'
-        from pathlib import Path
-
-        path = Path("MAD/src/Makefile")
-        text = path.read_text()
-
-        replacements = [
-            ("CC       := gcc-11", "CC       := gcc"),
-            ("CXX      := g++-11", "CXX      := g++"),
-            ("FC       := gfortran-11", "FC       := gfortran"),
-            ("-fdiagnostics-all-candidates", ""),
-            ("-flto", ""),
-            ("-march=native", ""),
-            ("-mtune=native", ""),
-            ("-mfma", ""),
-        ]
-
-        for old, new in replacements:
-            text = text.replace(old, new)
-
-        path.write_text(text)
-        PY
-
-    - name: Build MAD-NG dependencies
-      run: |
-        set -euo pipefail
-
-        export OS=macosx
-        export MACOSX_DEPLOYMENT_TARGET=11
-        export JOBS="$(sysctl -n hw.ncpu)"
-        export CC=gcc
-        export CXX=g++
-        export FC=gfortran
-        export AR=ar
-        export RANLIB=ranlib
-
-        mkdir -p MAD/tools
-        cp -f tools/build_madng_deps_linux.sh MAD/tools/ || true
-
-        mkdir -p MAD/bin/macosx
-
-        cd MAD/lib
-
-        rm -rf luajit
-        git clone https://github.com/MethodicalAcceleratorDesign/LuaJIT.git luajit
-        cd luajit
-        git checkout mad-patch
-        make clean || true
-        make -j"${JOBS}" amalg PREFIX="$(pwd)"
-        make install PREFIX="$(pwd)"
-        cp -f src/libluajit.a ../../bin/macosx/
-        cd ..
-
-        rm -rf lfs
-        git clone https://github.com/MethodicalAcceleratorDesign/luafilesystem.git lfs
-        cd lfs
-        make clean || true
-        make lfs.a
-        cp -f liblfs.a ../../bin/macosx/
-        cd ..
-
-        rm -rf lpeg lpeg-1.1.0 lpeg-1.1.0.tar.gz
-        curl -fsSL -o lpeg-1.1.0.tar.gz http://www.inf.puc-rio.br/~roberto/lpeg/lpeg-1.1.0.tar.gz
-        tar xzf lpeg-1.1.0.tar.gz
-        ln -s lpeg-1.1.0 lpeg
-        cd lpeg
-        python3 - <<'PY'
-        from pathlib import Path
-        import re
-
-        path = Path("makefile")
-        text = path.read_text()
-        text = re.sub(r"^LUADIR[ \t]*=.*$", "LUADIR = ../luajit/include/luajit-2.1", text, flags=re.MULTILINE)
-        text = re.sub(r"^LUALIB[ \t]*=.*$", "LUALIB = ../luajit/lib/libluajit-5.1.a", text, flags=re.MULTILINE)
-        text = re.sub(r"^COPT[ \t]*=.*$", "COPT = -O3 -DNDEBUG", text, flags=re.MULTILINE)
-        path.write_text(text)
-        PY
-        make clean || true
-        make -j"${JOBS}" CC=gcc LUADIR="../luajit/include/luajit-2.1" \
-          lpvm.o lpcap.o lptree.o lpcode.o lpprint.o lpcset.o
-        ar -r liblpeg.a lpvm.o lpcap.o lptree.o lpcode.o lpprint.o lpcset.o
-        ranlib liblpeg.a
-        cp -f liblpeg.a ../../bin/macosx/
-        cd ..
-
-        rm -rf lapack
-        git clone https://github.com/Reference-LAPACK/lapack lapack
-        cd lapack
-        cp -f make.inc.example make.inc
-        python3 - <<'PY'
-        from pathlib import Path
-        import re
-
-        path = Path("make.inc")
-        text = path.read_text()
-        for key in ("CFLAGS", "FFLAGS", "FFLAGS_NOOPT"):
-            text = re.sub(rf"^({key}[ \t]*=[ \t]*)(?!-fPIC\b)", r"\1-fPIC ", text, flags=re.MULTILINE)
-        path.write_text(text)
-        PY
-        make clean || true
-        make -j"${JOBS}" blaslib
-        make -j"${JOBS}" lapacklib
-        cp -f librefblas.a ../../bin/macosx/
-        cp -f liblapack.a ../../bin/macosx/
-        cd ..
-
-        rm -rf fftw3 fftw-3.3.10 fftw-3.3.10.tar.gz
-        curl -fsSL -o fftw-3.3.10.tar.gz https://www.fftw.org/fftw-3.3.10.tar.gz
-        tar xzf fftw-3.3.10.tar.gz
-        ln -s fftw-3.3.10 fftw3
-        cd fftw3
-        make clean || true
-        ./configure --disable-shared
-        make -j"${JOBS}"
-        cp -f .libs/libfftw3.a ../../bin/macosx/
-        cd ..
-
-        rm -rf nfft3 nfft-3.5.3 nfft-3.5.3.tar.gz
-        curl -fsSL -o nfft-3.5.3.tar.gz https://www-user.tu-chemnitz.de/~potts/nfft/download/nfft-3.5.3.tar.gz
-        tar xzf nfft-3.5.3.tar.gz
-        ln -s nfft-3.5.3 nfft3
-        cd nfft3
-        make clean || true
-        ./configure --enable-all --disable-shared \
-          --with-fftw3="$(pwd)/../fftw3" \
-          --with-fftw3-libdir="$(pwd)/../fftw3/.libs" \
-          --with-fftw3-includedir="$(pwd)/../fftw3/api"
-        make -j"${JOBS}"
-        cp -f .libs/libnfft3.a ../../bin/macosx/
-        cd ..
-
-        rm -rf nlopt
-        git clone https://github.com/stevengj/nlopt nlopt
-        cd nlopt
-        mkdir -p build
-        cd build
-        cmake -DBUILD_SHARED_LIBS=OFF -DNLOPT_CXX=OFF ..
-        make -j"${JOBS}"
-        cp -f libnlopt.a ../../../bin/macosx/
-
-    - name: Compile MAD-NG
-      working-directory: MAD/src
-      run: |
-        set -euo pipefail
-
-        which gcc
-        gcc --version
-        which g++
-        g++ --version
-        which gfortran
-        gfortran --version
-
-        make SHELL=/bin/bash CC=gcc CXX=g++ FC=gfortran
-
-        file mad
-        otool -L mad || true
-
-    - name: Upload binary
-      uses: actions/upload-artifact@v4
-      with:
-        name: mad-macOS-x86_64
-        path: MAD/src/mad
-        ln -sf "/usr/local/bin/make" "${toolshim}/make"
-        ln -sf "/usr/local/bin/cmake" "${toolshim}/cmake"
-        ln -sf "/usr/local/bin/pkg-config" "${toolshim}/pkg-config"
-        ln -sf "/usr/local/bin/libtool" "${toolshim}/libtool"
-        ln -sf "/usr/local/bin/ar" "${toolshim}/ar"
-        ln -sf "/usr/local/bin/ranlib" "${toolshim}/ranlib"
-
-        {
-          echo "${toolshim}"
-          echo "/usr/local/bin"
-          echo "$(arch -x86_64 /usr/local/bin/brew --prefix)/bin"
-        } >> "${GITHUB_PATH}"
-
-    - name: Select MAD-NG macOS Makefile
-      run: |
-        cp MAD/src/Makefile.macosx MAD/src/Makefile
-        python3 - <<'PY'
-        from pathlib import Path
-        path = Path("MAD/src/Makefile")
-        text = path.read_text()
-        replacements = [
-            ("CC       := gcc-11", "CC       := gcc"),
-            ("CXX      := g++-11", "CXX      := g++"),
-            ("FC       := gfortran-11", "FC       := gfortran"),
-            ("-fdiagnostics-all-candidates", ""),
-            ("-flto", ""),
-            ("-march=native", ""),
-            ("-mtune=native", ""),
-            ("-mfma", ""),
-        ]
-        for old, new in replacements:
-            text = text.replace(old, new)
-        path.write_text(text)
-        PY
-
-    - name: Build MAD-NG dependencies (README order)
-      run: |
-        set -euo pipefail
-
-        echo "== Toolchain =="
-        which gcc
-        gcc --version
-        which g++
-        g++ --version
-        which gfortran
-        gfortran --version
-
-        export OS=macosx
-        export MACOSX_DEPLOYMENT_TARGET=11
-        export JOBS="$(sysctl -n hw.ncpu)"
-        export CC=gcc
-        export CXX=g++
-        export FC=gfortran
-        export AR=ar
-        export RANLIB=ranlib
-        export CFLAGS="-arch x86_64"
-        export CXXFLAGS="-arch x86_64"
-        export FFLAGS="-arch x86_64"
-        export FCFLAGS="-arch x86_64"
-        export LDFLAGS="-arch x86_64"
-
-        mkdir -p MAD/bin/macosx
-
-        cd MAD/lib
-        echo "== MAD/lib contents (before download) =="
-        ls -la
-
-        echo "== LuaJIT (README.luajit) =="
-        rm -rf luajit
-        git clone https://github.com/MethodicalAcceleratorDesign/LuaJIT.git luajit
-        cd luajit
-        git checkout mad-patch
-        git pull
-        make clean
-        make -j"${JOBS}" amalg PREFIX="$(pwd)"
-        make install PREFIX="$(pwd)"
-        cp -f src/libluajit.a ../../bin/macosx/
-        cd ..
-
-        echo "== LFS (README.lfs) =="
-        rm -rf lfs
-        git clone https://github.com/MethodicalAcceleratorDesign/luafilesystem.git lfs
-        cd lfs
-        make clean || true
-        make lfs.a
-        cp -f liblfs.a ../../bin/macosx/
-        cd ..
-
-        echo "== LPEG (README.lpeg) =="
-        rm -rf lpeg lpeg-1.1.0 lpeg-1.1.0.tar.gz
-        curl -fsSL -o lpeg-1.1.0.tar.gz http://www.inf.puc-rio.br/~roberto/lpeg/lpeg-1.1.0.tar.gz
-        tar xvzf lpeg-1.1.0.tar.gz
-        ln -s lpeg-1.1.0 lpeg
-        cd lpeg
-        python3 - <<'PY'
-        from pathlib import Path
-        import re
-        path = Path("makefile")
-        text = path.read_text()
-        text = re.sub(r"^LUADIR[ \t]*=.*$", "LUADIR = ../luajit/include/luajit-2.1", text, flags=re.MULTILINE)
-        text = re.sub(r"^LUALIB[ \t]*=.*$", "LUALIB = ../luajit/lib/libluajit-5.1.a", text, flags=re.MULTILINE)
-        text = re.sub(r"^COPT[ \t]*=.*$", "COPT = -O3 -DNDEBUG", text, flags=re.MULTILINE)
-        path.write_text(text)
-        PY
-        make clean || true
-        make -j"${JOBS}" CC="${CC:-gcc}" LUADIR="../luajit/include/luajit-2.1" lpvm.o lpcap.o lptree.o lpcode.o lpprint.o lpcset.o
-        ar -r liblpeg.a lpvm.o lpcap.o lptree.o lpcode.o lpprint.o lpcset.o
-        ranlib liblpeg.a
-        cp -f liblpeg.a ../../bin/macosx/
-        cd ..
-
-        echo "== LAPACK (README.lapack) =="
-        rm -rf lapack
-        git clone https://github.com/Reference-LAPACK/lapack lapack
-        cd lapack
-        cp -f make.inc.example make.inc
-        python3 - <<'PY'
-        from pathlib import Path
-        import re
-        path = Path("make.inc")
-        text = path.read_text()
-        for key in ("CFLAGS", "FFLAGS", "FFLAGS_NOOPT"):
-            text = re.sub(rf"^({key}[ \t]*=[ \t]*)(?!-fPIC\b)", r"\1-fPIC ", text, flags=re.MULTILINE)
-        path.write_text(text)
-        PY
-        make clean || true
-        make -j"${JOBS}" blaslib
-        make -j"${JOBS}" lapacklib
-        cp -f librefblas.a ../../bin/macosx/
-        cp -f liblapack.a ../../bin/macosx/
-        cd ..
-
-        echo "== FFTW3 (README.fftw3) =="
-        rm -rf fftw3 fftw-3.3.10 fftw-3.3.10.tar.gz
-        curl -fsSL -o fftw-3.3.10.tar.gz ftp://ftp.fftw.org/pub/fftw/fftw-3.3.10.tar.gz
-        tar xvzf fftw-3.3.10.tar.gz
-        ln -s fftw-3.3.10 fftw3
-        cd fftw3
-        make clean || true
-        ./configure --disable-shared
-        make -j"${JOBS}"
-        cp -f .libs/libfftw3.a ../../bin/macosx/
-        cd ..
-
-        echo "== NFFT3 (README.nfft3) =="
-        rm -rf nfft3 nfft-3.5.3 nfft-3.5.3.tar.gz
-        curl -fsSL -o nfft-3.5.3.tar.gz https://www-user.tu-chemnitz.de/~potts/nfft/download/nfft-3.5.3.tar.gz
-        tar xvzf nfft-3.5.3.tar.gz
-        ln -s nfft-3.5.3 nfft3
-        cd nfft3
-        make clean || true
-        ./configure --enable-all --disable-shared \
-          --with-fftw3="$(pwd)"/../fftw3 \
-          --with-fftw3-libdir="$(pwd)"/../fftw3/.libs \
-          --with-fftw3-includedir="$(pwd)"/../fftw3/api
-        make -j"${JOBS}"
-        cp -f .libs/libnfft3.a ../../bin/macosx/
-        cd ..
-
-        echo "== NLOPT (README.nlopt) =="
-        rm -rf nlopt
-        git clone https://github.com/stevengj/nlopt nlopt
-        cd nlopt
-        rm -rf build
-        mkdir -p build
-        cd build
-        cmake -DBUILD_SHARED_LIBS=OFF -DNLOPT_CXX=OFF ..
-        make -j"${JOBS}"
-        cp -f libnlopt.a ../../../bin/macosx/
-
-    - name: Compile MAD-NG
-      working-directory: MAD/src
-      run: |
-        echo "== Toolchain =="
-        which gcc
-        gcc --version
-        which g++
-        g++ --version
-        which gfortran
-        gfortran --version
-
-        make SHELL=/bin/bash CC=gcc CXX=g++ FC=gfortran
-
-    - name: Upload binary
-      uses: actions/upload-artifact@v4
-      with:
-        name: mad-macOS-x86_64
-        path: MAD/src/mad
+      - name: Checkout current repo
+        uses: actions/checkout@v4
+
+      - name: Clone MAD-NG
+        uses: actions/checkout@v4
+        with:
+          repository: MethodicalAcceleratorDesign/MAD-NG
+          path: MAD
+          submodules: recursive
+
+      - name: Install build tools
+        run: |
+          brew update
+          brew install gcc@12 make cmake automake autoconf libtool pkg-config curl
+
+      - name: Prepare compiler shims
+        run: |
+          set -euo pipefail
+
+          gcc_prefix="$(brew --prefix gcc@12)"
+          toolshim="${RUNNER_TEMP}/gcc-shim"
+          mkdir -p "${toolshim}"
+
+          ln -sf "${gcc_prefix}/bin/gcc-12" "${toolshim}/gcc"
+          ln -sf "${gcc_prefix}/bin/g++-12" "${toolshim}/g++"
+          ln -sf "${gcc_prefix}/bin/gfortran-12" "${toolshim}/gfortran"
+          ln -sf "$(brew --prefix)/bin/make" "${toolshim}/make"
+          ln -sf "$(brew --prefix)/bin/cmake" "${toolshim}/cmake"
+          ln -sf "$(brew --prefix)/bin/pkg-config" "${toolshim}/pkg-config"
+          ln -sf "$(brew --prefix)/bin/libtool" "${toolshim}/libtool"
+          ln -sf "$(brew --prefix)/bin/ar" "${toolshim}/ar" || true
+          ln -sf "$(brew --prefix)/bin/ranlib" "${toolshim}/ranlib" || true
+
+          {
+            echo "${toolshim}"
+            echo "$(brew --prefix)/bin"
+          } >> "${GITHUB_PATH}"
+
+      - name: Select MAD-NG macOS Makefile
+        run: |
+          cp MAD/src/Makefile.macosx MAD/src/Makefile
+          python3 - <<'PY'
+          from pathlib import Path
+          path = Path("MAD/src/Makefile")
+          text = path.read_text()
+          replacements = [
+              ("CC       := gcc-11", "CC       := gcc"),
+              ("CXX      := g++-11", "CXX      := g++"),
+              ("FC       := gfortran-11", "FC       := gfortran"),
+              ("-fdiagnostics-all-candidates", ""),
+              ("-flto", ""),
+              ("-march=native", ""),
+              ("-mtune=native", ""),
+              ("-mfma", ""),
+          ]
+          for old, new in replacements:
+              text = text.replace(old, new)
+          path.write_text(text)
+          PY
+
+      - name: Build MAD-NG dependencies (README order)
+        run: |
+          set -euo pipefail
+
+          echo "== Toolchain =="
+          which gcc
+          gcc --version
+          which g++
+          g++ --version
+          which gfortran
+          gfortran --version
+
+          export OS=macosx
+          export MACOSX_DEPLOYMENT_TARGET=11
+          export JOBS="$(sysctl -n hw.ncpu)"
+          export CC=gcc
+          export CXX=g++
+          export FC=gfortran
+          export AR=ar
+          export RANLIB=ranlib
+
+          mkdir -p MAD/bin/macosx
+
+          cd MAD/lib
+          echo "== MAD/lib contents (before download) =="
+          ls -la
+
+          echo "== LuaJIT (README.luajit) =="
+          rm -rf luajit
+          git clone https://github.com/MethodicalAcceleratorDesign/LuaJIT.git luajit
+          cd luajit
+          git checkout mad-patch
+          git pull
+          make clean
+          make -j"${JOBS}" amalg PREFIX="$(pwd)"
+          make install PREFIX="$(pwd)"
+          cp -f src/libluajit.a ../../bin/macosx/
+          cd ..
+
+          echo "== LFS (README.lfs) =="
+          rm -rf lfs
+          git clone https://github.com/MethodicalAcceleratorDesign/luafilesystem.git lfs
+          cd lfs
+          make clean || true
+          make lfs.a
+          cp -f liblfs.a ../../bin/macosx/
+          cd ..
+
+          echo "== LPEG (README.lpeg) =="
+          rm -rf lpeg lpeg-1.1.0 lpeg-1.1.0.tar.gz
+          curl -fsSL -o lpeg-1.1.0.tar.gz http://www.inf.puc-rio.br/~roberto/lpeg/lpeg-1.1.0.tar.gz
+          tar xvzf lpeg-1.1.0.tar.gz
+          ln -s lpeg-1.1.0 lpeg
+          cd lpeg
+          python3 - <<'PY'
+          from pathlib import Path
+          import re
+          path = Path("makefile")
+          text = path.read_text()
+          text = re.sub(r"^LUADIR[ \t]*=.*$", "LUADIR = ../luajit/include/luajit-2.1", text, flags=re.MULTILINE)
+          text = re.sub(r"^LUALIB[ \t]*=.*$", "LUALIB = ../luajit/lib/libluajit-5.1.a", text, flags=re.MULTILINE)
+          text = re.sub(r"^COPT[ \t]*=.*$", "COPT = -O3 -DNDEBUG", text, flags=re.MULTILINE)
+          path.write_text(text)
+          PY
+          make clean || true
+          make -j"${JOBS}" CC="${CC:-gcc}" LUADIR="../luajit/include/luajit-2.1" lpvm.o lpcap.o lptree.o lpcode.o lpprint.o lpcset.o
+          ar -r liblpeg.a lpvm.o lpcap.o lptree.o lpcode.o lpprint.o lpcset.o
+          ranlib liblpeg.a
+          cp -f liblpeg.a ../../bin/macosx/
+          cd ..
+
+          echo "== LAPACK (README.lapack) =="
+          rm -rf lapack
+          git clone https://github.com/Reference-LAPACK/lapack lapack
+          cd lapack
+          cp -f make.inc.example make.inc
+          python3 - <<'PY'
+          from pathlib import Path
+          import re
+          path = Path("make.inc")
+          text = path.read_text()
+          for key in ("CFLAGS", "FFLAGS", "FFLAGS_NOOPT"):
+              text = re.sub(rf"^({key}[ \t]*=[ \t]*)(?!-fPIC\b)", r"\1-fPIC ", text, flags=re.MULTILINE)
+          path.write_text(text)
+          PY
+          make clean || true
+          make -j"${JOBS}" blaslib
+          make -j"${JOBS}" lapacklib
+          cp -f librefblas.a ../../bin/macosx/
+          cp -f liblapack.a ../../bin/macosx/
+          cd ..
+
+          echo "== FFTW3 (README.fftw3) =="
+          rm -rf fftw3 fftw-3.3.10 fftw-3.3.10.tar.gz
+          curl -fsSL -o fftw-3.3.10.tar.gz https://www.fftw.org/fftw-3.3.10.tar.gz
+          tar xvzf fftw-3.3.10.tar.gz
+          ln -s fftw-3.3.10 fftw3
+          cd fftw3
+          make clean || true
+          ./configure --disable-shared
+          make -j"${JOBS}"
+          cp -f .libs/libfftw3.a ../../bin/macosx/
+          cd ..
+
+          echo "== NFFT3 (README.nfft3) =="
+          rm -rf nfft3 nfft-3.5.3 nfft-3.5.3.tar.gz
+          curl -fsSL -o nfft-3.5.3.tar.gz https://www-user.tu-chemnitz.de/~potts/nfft/download/nfft-3.5.3.tar.gz
+          tar xvzf nfft-3.5.3.tar.gz
+          ln -s nfft-3.5.3 nfft3
+          cd nfft3
+          make clean || true
+          ./configure --enable-all --disable-shared \
+            --with-fftw3="$(pwd)"/../fftw3 \
+            --with-fftw3-libdir="$(pwd)"/../fftw3/.libs \
+            --with-fftw3-includedir="$(pwd)"/../fftw3/api
+          make -j"${JOBS}"
+          cp -f .libs/libnfft3.a ../../bin/macosx/
+          cd ..
+
+          echo "== NLOPT (README.nlopt) =="
+          rm -rf nlopt
+          git clone https://github.com/stevengj/nlopt nlopt
+          cd nlopt
+          rm -rf build
+          mkdir -p build
+          cd build
+          cmake -DBUILD_SHARED_LIBS=OFF -DNLOPT_CXX=OFF ..
+          make -j"${JOBS}"
+          cp -f libnlopt.a ../../../bin/macosx/
+
+      - name: Compile MAD-NG
+        working-directory: MAD/src
+        run: |
+          set -euo pipefail
+
+          echo "== Toolchain =="
+          which gcc
+          gcc --version
+          which g++
+          g++ --version
+          which gfortran
+          gfortran --version
+
+          make SHELL=/bin/bash CC=gcc CXX=g++ FC=gfortran
+
+          file mad
+          otool -L mad || true
+
+      - name: Upload binary
+        uses: actions/upload-artifact@v4
+        with:
+          name: mad-macOS-x86_64
+          path: MAD/src/mad

From 29099d1df5c09030a4f6752891586e8d1dd2c67e Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 15:34:45 +0200
Subject: [PATCH 66/69] not use premium runner

---
 .github/workflows/compile_madng.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 6be78ad..df6114c 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -71,7 +71,7 @@ jobs:
           path: MAD/src/mad
 
   build-macos-x86_64:
-    runs-on: macos-14-large
+    runs-on: macos-13
     defaults:
       run:
         shell: bash

From e427593ca87f2e639b24c102bbde60e6ecb14985 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Thu, 14 May 2026 15:43:11 +0200
Subject: [PATCH 67/69] Update compile_madng.yml

---
 .github/workflows/compile_madng.yml | 25 ++++++++++++-------------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index df6114c..48b63f0 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -71,7 +71,7 @@ jobs:
           path: MAD/src/mad
 
   build-macos-x86_64:
-    runs-on: macos-13
+    runs-on: macos-15-intel
     defaults:
       run:
         shell: bash
@@ -103,15 +103,16 @@ jobs:
           ln -sf "${gcc_prefix}/bin/gcc-12" "${toolshim}/gcc"
           ln -sf "${gcc_prefix}/bin/g++-12" "${toolshim}/g++"
           ln -sf "${gcc_prefix}/bin/gfortran-12" "${toolshim}/gfortran"
-          ln -sf "$(brew --prefix)/bin/make" "${toolshim}/make"
-          ln -sf "$(brew --prefix)/bin/cmake" "${toolshim}/cmake"
-          ln -sf "$(brew --prefix)/bin/pkg-config" "${toolshim}/pkg-config"
-          ln -sf "$(brew --prefix)/bin/libtool" "${toolshim}/libtool"
-          ln -sf "$(brew --prefix)/bin/ar" "${toolshim}/ar" || true
-          ln -sf "$(brew --prefix)/bin/ranlib" "${toolshim}/ranlib" || true
+          ln -sf "/usr/local/bin/make" "${toolshim}/make"
+          ln -sf "/usr/local/bin/cmake" "${toolshim}/cmake"
+          ln -sf "/usr/local/bin/pkg-config" "${toolshim}/pkg-config"
+          ln -sf "/usr/local/bin/libtool" "${toolshim}/libtool"
+          ln -sf "/usr/local/bin/ar" "${toolshim}/ar"
+          ln -sf "/usr/local/bin/ranlib" "${toolshim}/ranlib"
 
           {
             echo "${toolshim}"
+            echo "/usr/local/bin"
             echo "$(brew --prefix)/bin"
           } >> "${GITHUB_PATH}"
 
@@ -120,6 +121,7 @@ jobs:
           cp MAD/src/Makefile.macosx MAD/src/Makefile
           python3 - <<'PY'
           from pathlib import Path
+
           path = Path("MAD/src/Makefile")
           text = path.read_text()
           replacements = [
@@ -194,6 +196,7 @@ jobs:
           python3 - <<'PY'
           from pathlib import Path
           import re
+
           path = Path("makefile")
           text = path.read_text()
           text = re.sub(r"^LUADIR[ \t]*=.*$", "LUADIR = ../luajit/include/luajit-2.1", text, flags=re.MULTILINE)
@@ -216,6 +219,7 @@ jobs:
           python3 - <<'PY'
           from pathlib import Path
           import re
+
           path = Path("make.inc")
           text = path.read_text()
           for key in ("CFLAGS", "FFLAGS", "FFLAGS_NOOPT"):
@@ -231,7 +235,7 @@ jobs:
 
           echo "== FFTW3 (README.fftw3) =="
           rm -rf fftw3 fftw-3.3.10 fftw-3.3.10.tar.gz
-          curl -fsSL -o fftw-3.3.10.tar.gz https://www.fftw.org/fftw-3.3.10.tar.gz
+          curl -fsSL -o fftw-3.3.10.tar.gz ftp://ftp.fftw.org/pub/fftw/fftw-3.3.10.tar.gz
           tar xvzf fftw-3.3.10.tar.gz
           ln -s fftw-3.3.10 fftw3
           cd fftw3
@@ -270,8 +274,6 @@ jobs:
       - name: Compile MAD-NG
         working-directory: MAD/src
         run: |
-          set -euo pipefail
-
           echo "== Toolchain =="
           which gcc
           gcc --version
@@ -282,9 +284,6 @@ jobs:
 
           make SHELL=/bin/bash CC=gcc CXX=g++ FC=gfortran
 
-          file mad
-          otool -L mad || true
-
       - name: Upload binary
         uses: actions/upload-artifact@v4
         with:

From 1feefdd5a9a7f0464e27e37fc8f56078ba2ba6a4 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Sat, 11 Jul 2026 21:34:00 +0200
Subject: [PATCH 68/69] Make it so that the compilation yaml can be used while
 publishing to pypi.

---
 .github/workflows/compile_madng.yml  |  2 ++
 .github/workflows/python-publish.yml | 35 ++++++++++++++++++++++++----
 2 files changed, 33 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/compile_madng.yml b/.github/workflows/compile_madng.yml
index 48b63f0..06e76a4 100644
--- a/.github/workflows/compile_madng.yml
+++ b/.github/workflows/compile_madng.yml
@@ -3,6 +3,8 @@ name: Make a MAD-NG Binary
 on:
   push:
   workflow_dispatch:
+  # Allow release workflows to build and consume these exact binaries.
+  workflow_call:
 
 jobs:
   build-linux:
diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
index 0117067..93fa29f 100644
--- a/.github/workflows/python-publish.yml
+++ b/.github/workflows/python-publish.yml
@@ -16,7 +16,15 @@ permissions:
   contents: read
 
 jobs:
+  # Set the repository variable PYMADNG_BUILD_MADNG_FROM_SOURCE to "false"
+  # to temporarily restore the legacy pre-built binary download path below.
+  compile-madng:
+    if: ${{ vars.PYMADNG_BUILD_MADNG_FROM_SOURCE != 'false' }}
+    uses: ./.github/workflows/compile_madng.yml
+
   deploy:
+    needs: compile-madng
+    if: ${{ always() && (needs.compile-madng.result == 'success' || needs.compile-madng.result == 'skipped') }}
     runs-on: ubuntu-latest
     # Specifying a GitHub environment is optional, but strongly encouraged
     environment: release
@@ -34,11 +42,30 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install build
-    - name: Get MAD Binaries
+    - name: Download compiled Linux MAD-NG
+      if: ${{ vars.PYMADNG_BUILD_MADNG_FROM_SOURCE != 'false' }}
+      uses: actions/download-artifact@v5
+      with:
+        name: mad-Linux
+        path: build/mad-Linux
+    - name: Download compiled macOS MAD-NG
+      if: ${{ vars.PYMADNG_BUILD_MADNG_FROM_SOURCE != 'false' }}
+      uses: actions/download-artifact@v5
+      with:
+        name: mad-macOS-x86_64
+        path: build/mad-Darwin
+    - name: Add compiled MAD-NG binaries to the package
+      if: ${{ vars.PYMADNG_BUILD_MADNG_FROM_SOURCE != 'false' }}
+      run: |
+        mkdir -p src/pymadng/bin
+        install -m 755 build/mad-Linux/mad src/pymadng/bin/mad_Linux
+        install -m 755 build/mad-Darwin/mad src/pymadng/bin/mad_Darwin
+    - name: Download pre-built MAD-NG binaries (legacy fallback)
+      if: ${{ vars.PYMADNG_BUILD_MADNG_FROM_SOURCE == 'false' }}
       run: |
-        mkdir src/pymadng/bin
-        curl https://madx.web.cern.ch/releases/madng/1.1/mad-linux-1.1.13 -o src/pymadng/bin/mad_Linux
-        curl https://madx.web.cern.ch/releases/madng/1.1/mad-macos-1.1.13 -o src/pymadng/bin/mad_Darwin
+        mkdir -p src/pymadng/bin
+        curl --fail --location https://madx.web.cern.ch/releases/madng/1.1/mad-linux-1.1.13 -o src/pymadng/bin/mad_Linux
+        curl --fail --location https://madx.web.cern.ch/releases/madng/1.1/mad-macos-1.1.13 -o src/pymadng/bin/mad_Darwin
         chmod +x src/pymadng/bin/mad_Linux src/pymadng/bin/mad_Darwin
     - name: Build package
       run: python -m build

From 522157c60916b60da510ca7049eeb26c86929a66 Mon Sep 17 00:00:00 2001
From: Joshua Gray <61458311+jgray-19@users.noreply.github.com>
Date: Sat, 11 Jul 2026 21:40:14 +0200
Subject: [PATCH 69/69] Update readme and remove unnecessary script

---
 tools/README.deps.md               |  81 ++++--------
 tools/stage_madng_headers_linux.sh | 205 -----------------------------
 2 files changed, 28 insertions(+), 258 deletions(-)
 delete mode 100755 tools/stage_madng_headers_linux.sh

diff --git a/tools/README.deps.md b/tools/README.deps.md
index 5275bae..f5b424d 100644
--- a/tools/README.deps.md
+++ b/tools/README.deps.md
@@ -1,66 +1,41 @@
-# MAD-NG dependency build scripts
+# Building MAD-NG dependencies
 
-These scripts download/build the third-party **static** libraries MAD-NG expects, and copy the resulting `*.a` files into the OS-specific `bin/` directory (matching the historical layout in `my_lib/`).
+This directory contains the Linux dependency builder used by the MAD-NG
+compile workflow. It builds static third-party libraries from source; it does
+not build or publish `pymadng` itself.
 
-## Linux
+## Release route
 
-```bash
-chmod +x tools/build_madng_deps_linux.sh
-./tools/build_madng_deps_linux.sh
-```
-
-Outputs into `bin/linux/`:
-
-- `libluajit.a`
-- `liblfs.a`
-- `liblpeg.a`
-- `liblapack.a`
-- `librefblas.a`
-- `libfftw3.a`
-- `libnfft3.a`
-- `libnlopt.a`
+Publishing a GitHub release runs these workflows in order:
 
-## macOS
+1. `python-publish.yml` calls `compile_madng.yml`.
+2. The Linux job copies this script into the checked-out MAD-NG source and runs
+   it. The macOS job builds its dependencies directly in the workflow.
+3. Both jobs compile MAD-NG and upload a `mad` artifact.
+4. The publish job installs the artifacts as
+   `src/pymadng/bin/mad_Linux` and `src/pymadng/bin/mad_Darwin`, builds the
+   Python distributions, and publishes them to PyPI.
 
-Prereqs (typical Homebrew setup):
+To temporarily use the old pre-built-download route, set the GitHub repository
+variable `PYMADNG_BUILD_MADNG_FROM_SOURCE` to `false`. Delete the variable, or
+set it to any other value, to compile from source again.
 
-```bash
-brew install cmake gcc make automake libtool pkg-config
-```
+## Manual Linux route
 
-Then:
+Run the script from the root of a MAD-NG checkout:
 
 ```bash
-chmod +x tools/build_madng_deps_macos.sh
-./tools/build_madng_deps_macos.sh
+JOBS="$(nproc)" CC=gcc CXX=g++ FC=gfortran \
+  AR=ar RANLIB=ranlib ./tools/build_madng_deps_linux.sh
 ```
 
-Outputs into `bin/macosx/` (same filenames as Linux).
-
-## “Fill in the necessary things”
-
-All knobs can be supplied as environment variables (no prompts), or left unset to be prompted:
-
-- Build tools: `JOBS`, `CC`, `CXX`, `FC`, `AR`, `RANLIB`
-- LuaJIT: `LUAJIT_REPO`, `LUAJIT_REF`
-- LuaFileSystem: `LFS_REPO`, `LFS_REF`
-- Versions/refs: `LPEG_VERSION`, `FFTW_VERSION`, `NFFT_VERSION`, `NLOPT_REF`, `LAPACK_REF`
-- macOS only: `MACOSX_DEPLOYMENT_TARGET`
-
-Example (Linux):
-
-```bash
-JOBS=16 CC=clang FC=gfortran LUAJIT_REF=mad-patch ./tools/build_madng_deps_linux.sh
-```
-
-## Header-only staging (no rebuild)
-
-If you already have `*.a` archives in `bin/linux` or `bin/macosx`, but your build
-fails on missing headers (e.g. `lua.h`, `fftw3.h`, `nlopt.h`), use:
+If an option is omitted, the script prompts for it and suggests a default.
+It downloads sources into `lib/` and writes these archives to `bin/linux/`:
 
-- `tools/stage_madng_headers_linux.sh`
-- `tools/stage_madng_headers_macos.sh`
+- `libluajit.a`, `liblfs.a`, `liblpeg.a`
+- `liblapack.a`, `librefblas.a`
+- `libfftw3.a`, `libnfft3.a`, `libnlopt.a`
 
-They populate `lib/luajit`, `lib/nlopt`, `lib/fftw3`, `lib/nfft3` with the
-expected header layout (by cloning/downloading sources, or by symlinking from
-your provided include directories).
+Source versions and repositories can be overridden with `LUAJIT_REPO`,
+`LUAJIT_REF`, `LFS_REPO`, `LFS_REF`, `LPEG_VERSION`, `FFTW_VERSION`,
+`NFFT_VERSION`, `NLOPT_REF`, and `LAPACK_REF`.
diff --git a/tools/stage_madng_headers_linux.sh b/tools/stage_madng_headers_linux.sh
deleted file mode 100755
index e5c8f11..0000000
--- a/tools/stage_madng_headers_linux.sh
+++ /dev/null
@@ -1,205 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-
-# Stage headers into the layout expected by MAD-NG's unmodified `src/Makefile`.
-# The fetch/stage layout follows the documented MAD dependency build flow.
-#
-# Expected include paths (from `src/Makefile`):
-#   -I../lib/luajit/src            -> lua.h, luajit.h, luaconf.h, lualib.h, lauxlib.h, lua.hpp
-#   -I../lib/nlopt/src/api         -> nlopt.h
-#   -I../lib/fftw3/api             -> fftw3.h
-#   -I../lib/nfft3/include         -> nfft3.h (and friends)
-#
-# This script does NOT build archives; it only ensures headers exist (by
-# downloading sources, or by symlinking/copying from user-provided locations).
-
-ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
-LIB_DIR="${ROOT}/lib"
-LUAJIT_REF="${LUAJIT_REF:-mad-patch}"
-LUAJIT_REPO="${LUAJIT_REPO:-https://github.com/MethodicalAcceleratorDesign/LuaJIT.git}"
-
-NLOPT_REF="${NLOPT_REF:-v2.7.1}"
-NLOPT_REPO="${NLOPT_REPO:-https://github.com/stevengj/nlopt.git}"
-
-FFTW_VERSION="${FFTW_VERSION:-3.3.10}"
-NFFT_VERSION="${NFFT_VERSION:-3.5.3}"
-
-# Optional: point these at already-installed headers (will be copied/symlinked)
-LUAJIT_SRC_DIR="${LUAJIT_SRC_DIR:-}"   # directory containing lua.h, luajit.h, etc
-NLOPT_INC_DIR="${NLOPT_INC_DIR:-}"     # directory containing nlopt.h
-FFTW_INC_DIR="${FFTW_INC_DIR:-}"       # directory containing fftw3.h
-NFFT_INC_DIR="${NFFT_INC_DIR:-}"       # directory containing nfft3.h
-
-need_cmd() {
-  command -v "$1" >/dev/null 2>&1 || { echo "Missing command: $1" >&2; exit 1; }
-}
-
-pick_make() {
-  if command -v gmake >/dev/null 2>&1; then
-    echo "gmake"
-  else
-    echo "make"
-  fi
-}
-
-fetch_tarball() {
-  local url="$1"
-  local out="$2"
-  if [[ -f "${out}" ]]; then return 0; fi
-  if command -v curl >/dev/null 2>&1; then
-    curl -L --fail "${url}" -o "${out}"
-  else
-    need_cmd wget
-    wget -O "${out}" "${url}"
-  fi
-}
-
-stage_dir_copy_or_link() {
-  local src="$1"
-  local dest="$2"
-  local mode="${3:-symlink}" # symlink|copy
-  rm -rf "${dest}"
-  mkdir -p "$(dirname "${dest}")"
-  case "${mode}" in
-    symlink) ln -s "${src}" "${dest}" ;;
-    copy) cp -a "${src}" "${dest}" ;;
-    *) echo "Unknown mode: ${mode}" >&2; exit 1 ;;
-  esac
-}
-
-stage_file_copy_or_link() {
-  local src="$1"
-  local dest="$2"
-  local mode="${3:-symlink}" # symlink|copy
-  rm -f "${dest}"
-  mkdir -p "$(dirname "${dest}")"
-  case "${mode}" in
-    symlink) ln -s "${src}" "${dest}" ;;
-    copy) cp -a "${src}" "${dest}" ;;
-    *) echo "Unknown mode: ${mode}" >&2; exit 1 ;;
-  esac
-}
-
-main() {
-  mkdir -p "${LIB_DIR}"
-
-  # LuaJIT headers -> lib/luajit/src/*
-  if [[ -n "${LUAJIT_SRC_DIR}" ]]; then
-    echo "Staging LuaJIT headers from LUAJIT_SRC_DIR=${LUAJIT_SRC_DIR}"
-    [[ -e "${LUAJIT_SRC_DIR}/lua.h" ]] || { echo "Missing ${LUAJIT_SRC_DIR}/lua.h" >&2; exit 1; }
-    [[ -e "${LUAJIT_SRC_DIR}/luajit.h" ]] || { echo "Missing ${LUAJIT_SRC_DIR}/luajit.h" >&2; exit 1; }
-    mkdir -p "${LIB_DIR}/luajit"
-    stage_dir_copy_or_link "${LUAJIT_SRC_DIR}" "${LIB_DIR}/luajit/src" "symlink"
-  else
-    echo "Fetching LuaJIT repo for headers (${LUAJIT_REF})"
-    need_cmd git
-    local_dir="${LIB_DIR}/luajit"
-    if [[ ! -d "${local_dir}/.git" ]]; then
-      git clone "${LUAJIT_REPO}" "${local_dir}"
-    fi
-    ( cd "${local_dir}"
-      git fetch --all --tags
-      git checkout "${LUAJIT_REF}"
-      git pull --ff-only || true
-    )
-
-    # Follow `README.luajit` literally enough to materialize `src/luajit.h`:
-    #   make clean
-    #   make amalg PREFIX=`pwd`
-    #   make install PREFIX=`pwd`
-    if [[ ! -e "${local_dir}/src/luajit.h" ]]; then
-      echo "luajit.h not in repo — building LuaJIT as documented by MAD..."
-      mk="$(pick_make)"
-      (
-        cd "${local_dir}"
-        "${mk}" clean
-        "${mk}" amalg PREFIX="$(pwd)"
-        "${mk}" install PREFIX="$(pwd)"
-      )
-    fi
-  fi
-
-  # NLOpt headers -> lib/nlopt/src/api/nlopt.h
-  if [[ -n "${NLOPT_INC_DIR}" ]]; then
-    echo "Staging NLOpt header from NLOPT_INC_DIR=${NLOPT_INC_DIR}"
-    stage_file_copy_or_link "${NLOPT_INC_DIR}/nlopt.h" "${LIB_DIR}/nlopt/src/api/nlopt.h" "symlink"
-  else
-    echo "Fetching NLOpt repo for headers (${NLOPT_REF})"
-    need_cmd git
-    local_dir="${LIB_DIR}/nlopt"
-    if [[ ! -d "${local_dir}/.git" ]]; then
-      git clone "${NLOPT_REPO}" "${local_dir}"
-    fi
-    ( cd "${local_dir}"
-      git fetch --all --tags
-      git checkout "${NLOPT_REF}"
-      git pull --ff-only 2>/dev/null || true
-    )
-  fi
-
-  # FFTW headers -> lib/fftw3/api/fftw3.h
-  if [[ -n "${FFTW_INC_DIR}" ]]; then
-    echo "Staging FFTW header from FFTW_INC_DIR=${FFTW_INC_DIR}"
-    stage_file_copy_or_link "${FFTW_INC_DIR}/fftw3.h" "${LIB_DIR}/fftw3/api/fftw3.h" "symlink"
-  else
-    echo "Fetching FFTW tarball for headers (${FFTW_VERSION})"
-    need_cmd tar
-    tar_name="fftw-${FFTW_VERSION}.tar.gz"
-    tar_path="${LIB_DIR}/${tar_name}"
-    url="https://fftw.org/${tar_name}"
-    fetch_tarball "${url}" "${tar_path}"
-    ( cd "${LIB_DIR}" && tar xzf "${tar_name}" )
-    rm -rf "${LIB_DIR}/fftw3"
-    mkdir -p "${LIB_DIR}/fftw3/api"
-    if [[ -e "${LIB_DIR}/fftw-${FFTW_VERSION}/api/fftw3.h" ]]; then
-      ln -s "${LIB_DIR}/fftw-${FFTW_VERSION}/api/fftw3.h" "${LIB_DIR}/fftw3/api/fftw3.h"
-    else
-      ln -s "${LIB_DIR}/fftw-${FFTW_VERSION}/fftw3.h" "${LIB_DIR}/fftw3/api/fftw3.h"
-    fi
-  fi
-
-  # NFFT headers -> lib/nfft3/include/nfft3.h
-  if [[ -n "${NFFT_INC_DIR}" ]]; then
-    echo "Staging NFFT header from NFFT_INC_DIR=${NFFT_INC_DIR}"
-    mkdir -p "${LIB_DIR}/nfft3"
-    stage_dir_copy_or_link "${NFFT_INC_DIR}" "${LIB_DIR}/nfft3/include" "symlink"
-  else
-    echo "Fetching NFFT tarball for headers (${NFFT_VERSION})"
-    need_cmd tar
-    tar_name="nfft-${NFFT_VERSION}.tar.gz"
-    tar_path="${LIB_DIR}/${tar_name}"
-    url="https://www-user.tu-chemnitz.de/~potts/nfft/download/${tar_name}"
-    fetch_tarball "${url}" "${tar_path}"
-    ( cd "${LIB_DIR}" && tar xzf "${tar_name}" )
-    rm -rf "${LIB_DIR}/nfft3"
-    mkdir -p "${LIB_DIR}/nfft3/include"
-    if [[ -d "${LIB_DIR}/nfft-${NFFT_VERSION}/include" ]]; then
-      for header in "${LIB_DIR}"/nfft-"${NFFT_VERSION}"/include/*; do
-        ln -s "${header}" "${LIB_DIR}/nfft3/include/$(basename "${header}")"
-      done
-    else
-      ln -s "${LIB_DIR}/nfft-${NFFT_VERSION}/nfft3.h" "${LIB_DIR}/nfft3/include/nfft3.h"
-    fi
-  fi
-
-  echo
-  echo "Header checks (expected by src/Makefile):"
-  local rc=0
-  for f in \
-    "${LIB_DIR}/luajit/src/lua.h" \
-    "${LIB_DIR}/luajit/src/luajit.h" \
-    "${LIB_DIR}/nlopt/src/api/nlopt.h" \
-    "${LIB_DIR}/fftw3/api/fftw3.h" \
-    "${LIB_DIR}/nfft3/include/nfft3.h"
-  do
-    if [[ -e "${f}" ]]; then
-      echo "  OK  ${f}"
-    else
-      echo "  MISS ${f}" >&2
-      rc=1
-    fi
-  done
-  return "${rc}"
-}
-
-main "$@"