diff --git a/.github/workflows/cont_int.yml b/.github/workflows/cont_int.yml
index 98a0ac5263..49f57e2aaa 100644
--- a/.github/workflows/cont_int.yml
+++ b/.github/workflows/cont_int.yml
@@ -11,6 +11,8 @@ on:
   schedule:
     - cron: '0 0 * * *'
 
+env:
+  RMG_PY_COMMIT: 55464c54d1fa61b531e865682df598d33718597d
 
 jobs:
   build:
@@ -37,22 +39,28 @@ jobs:
     - name: Cache RMG-Py
       id: cache-rmg-py
       uses: actions/cache@v3
-      env:
-        CACHE_NUMBER: 2
       with:
         path: RMG-Py
-        key: ${{ runner.os }}-rmg-main
+        key: ${{ runner.os }}-rmg-${{ env.RMG_PY_COMMIT }}
         restore-keys: |
           ${{ runner.os }}-rmg-
 
-    - name: Checkout RMG-py
+    # - name: Checkout RMG-Py at specific commit
+    #   if: steps.cache-rmg-py.outputs.cache-hit != 'true'
+    #   uses: actions/checkout@v3
+    #   with:
+    #     repository: ReactionMechanismGenerator/RMG-Py
+    #     path: RMG-Py
+    #     ref: ${{ env.RMG_PY_COMMIT }}^1
+    #     fetch-depth: 0
+
+    - name: Clone & checkout RMG-Py at specific SHA
       if: steps.cache-rmg-py.outputs.cache-hit != 'true'
-      uses: actions/checkout@v3
-      with:
-        repository: ReactionMechanismGenerator/RMG-Py
-        path: RMG-Py
-        ref: main
-        fetch-depth: 1
+      run: |
+        git clone --filter=blob:none --no-checkout https://github.com/ReactionMechanismGenerator/RMG-Py.git RMG-Py
+        cd RMG-Py
+        git fetch --no-tags --prune origin ${RMG_PY_COMMIT}
+        git checkout --detach ${RMG_PY_COMMIT}
 
     - name: Cache RMG-database
       id: cache-rmg-db
@@ -64,6 +72,7 @@ jobs:
           key: ${{ runner.os }}-rmgdb-main
           restore-keys: |
             ${{ runner.os }}-rmgdb-
+
     - name: Checkout RMG-database
       if: steps.cache-rmg-db.outputs.cache-hit != 'true'
       uses: actions/checkout@v3
@@ -71,7 +80,7 @@ jobs:
         repository: ReactionMechanismGenerator/RMG-database
         path: RMG-database
         ref: main
-        fetch-depth: 1
+        fetch-depth: 0
 
     - name: Cache AutoTST
       id: cache-autotst
@@ -135,7 +144,7 @@ jobs:
           ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
 
     - name: Set up miniconda
-      uses: conda-incubator/setup-miniconda@v3
+      uses: conda-incubator/setup-miniconda@v3.2.0
       with:
           auto-update-conda: true
           environment-file: environment.yml
diff --git a/.github/workflows/update-cache.yml b/.github/workflows/update-cache.yml
index ba9f15e8f4..dfce1d1114 100644
--- a/.github/workflows/update-cache.yml
+++ b/.github/workflows/update-cache.yml
@@ -2,128 +2,136 @@ name: Update cache
 
 on:
   schedule:
-    - cron: "0 0 */7 * *"
+    - cron: '0 0 */7 * *'
   push:
-    branches:
-      - main
+    branches: [ main ]
 
 jobs:
   update_cache:
     runs-on: ubuntu-latest
     defaults:
       run:
-          shell: bash -el {0}
+        shell: bash -el {0}
+
     steps:
+      # ────────── source repo ──────────
       - name: Checkout ARC
-        uses: actions/checkout@v3
-        
+        uses: actions/checkout@v4
+
+      # ────────── RMG‑Py ──────────
       - name: Cache RMG
         id: cache-rmg
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
-            path: RMG-Py
-            key: ${{ runner.os }}-rmg-main
-
-      - name: Checkout RMG
-        uses: actions/checkout@v3
+          path: RMG-Py
+          key: ${{ runner.os }}-rmg-main
+          restore-keys: |
+            ${{ runner.os }}-rmg-
+      - name: Checkout RMG-Py
+        if: steps.cache-rmg.outputs.cache-hit != 'true'
+        uses: actions/checkout@v4
         with:
-            repository: ReactionMechanismGenerator/RMG-Py
-            path: RMG-Py
-            ref: main
-            fetch-depth: 1
+          repository: ReactionMechanismGenerator/RMG-Py
+          path: RMG-Py
+          ref: 55464c54d1fa61b531e865682df598d33718597d
+          fetch-depth: 1
 
+      # ────────── RMG‑database ──────────
       - name: Cache RMG-database
         id: cache-rmg-db
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
-            path: RMG-database
-            key: ${{ runner.os }}-rmgdb-main
-
+          path: RMG-database
+          key: ${{ runner.os }}-rmgdb-main
+          restore-keys: |
+            ${{ runner.os }}-rmgdb-
       - name: Checkout RMG-database
-        uses: actions/checkout@v3
+        if: steps.cache-rmg-db.outputs.cache-hit != 'true'
+        uses: actions/checkout@v4
         with:
-            repository: ReactionMechanismGenerator/RMG-database
-            path: RMG-database
-            ref: main
-            fetch-depth: 1
-        
+          repository: ReactionMechanismGenerator/RMG-database
+          path: RMG-database
+          ref: main
+          fetch-depth: 1
+
+      # ────────── AutoTST ──────────
       - name: Cache AutoTST
         id: cache-autotst
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
-            path: AutoTST
-            key: ${{ runner.os }}-autotst-main
-            restore-keys: |
-                ${{ runner.os }}-autotst-
+          path: AutoTST
+          key: ${{ runner.os }}-autotst-main
+          restore-keys: |
+            ${{ runner.os }}-autotst-
       - name: Checkout AutoTST
         if: steps.cache-autotst.outputs.cache-hit != 'true'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
-            repository: ReactionMechanismGenerator/AutoTST
-            path: AutoTST
-            ref: main
-            fetch-depth: 1
-    
+          repository: ReactionMechanismGenerator/AutoTST
+          path: AutoTST
+          ref: main
+          fetch-depth: 1
+
+      # ────────── TS‑GCN ──────────
       - name: Cache TS-GCN
         id: cache-tsgcn
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
-            path: TS-GCN
-            key: ${{ runner.os }}-tsgcn-main
-            restore-keys: |
-                ${{ runner.os }}-tsgcn-
+          path: TS-GCN
+          key: ${{ runner.os }}-tsgcn-main
+          restore-keys: |
+            ${{ runner.os }}-tsgcn-
       - name: Checkout TS-GCN
         if: steps.cache-tsgcn.outputs.cache-hit != 'true'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
-            repository: ReactionMechanismGenerator/TS-GCN
-            path: TS-GCN
-            ref: main
-            fetch-depth: 1
-        
+          repository: ReactionMechanismGenerator/TS-GCN
+          path: TS-GCN
+          ref: main
+          fetch-depth: 1
+
+      # ────────── KinBot ──────────
       - name: Cache KinBot
         id: cache-kinbot
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
-            path: KinBot
-            key: ${{ runner.os }}-kinbot-2.0.6
-            restore-keys: |
-                ${{ runner.os }}-kinbot-
-    
-      - name: Checkout Kinbot 2.0.6
+          path: KinBot
+          key: ${{ runner.os }}-kinbot-2.0.6
+          restore-keys: |
+            ${{ runner.os }}-kinbot-
+      - name: Checkout KinBot 2.0.6
         if: steps.cache-kinbot.outputs.cache-hit != 'true'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
-            repository: zadorlab/KinBot
-            path: KinBot
-            ref: v2.0.6
-            fetch-depth: 1
-    
-      - name: Cache Packages Packages
-        uses: actions/cache@v2
-        env:
-            CACHE_NUMBER: 0
+          repository: zadorlab/KinBot
+          path: KinBot
+          ref: v2.0.6
+          fetch-depth: 1
+
+      # ────────── Conda package cache ──────────
+      - name: Cache Conda packages
+        id: cache-conda-pkgs
+        uses: actions/cache@v4
         with:
-            path: ~/conda_pkgs_dir
-            key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
+          path: ~/conda_pkgs_dir
+          key: ${{ runner.os }}-conda-0-${{ hashFiles('environment.yml') }}
+
+      # ────────── Create / restore env ──────────
       - name: Setup ARC Env
-        uses: conda-incubator/setup-miniconda@v3
+        uses: conda-incubator/setup-miniconda@v3.2.0
         with:
-            auto-update-conda: true
-            environment-file: environment.yml
-            activate-environment: arc_env
-            miniconda-version: latest
-            conda-solver: libmamba
-    
+          auto-update-conda: true
+          environment-file: environment.yml
+          activate-environment: arc_env
+          miniconda-version: latest
+          conda-solver: libmamba
+
+      # ────────── Update env & save to cache ──────────
+      - name: Update environment
+        run: mamba env update -n arc_env -f environment.yml
+
       - name: Cache ARC env
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
-            path: ${{ env.CONDA }}/envs
-            key: conda-${{ runner.os }}--${{ runner.arch }}--${{ env.CACHE_NUMBER}}
-        env:
-            # Increase this value to reset cache if etc/example-environment.yml has not changed
-            CACHE_NUMBER: 0
-        id: cache-arc-env
-      - name: Update environment
-        run: conda env update -n arc_env -f environment.yml
-        if: steps.cache-arc-env.outputs.cache-hit != 'true'
+          path: ${{ env.CONDA }}/envs
+          key: conda-${{ runner.os }}-${{ runner.arch }}-0
diff --git a/Dockerfile b/Dockerfile
index 143d083b13..643470ad58 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -46,7 +46,7 @@ RUN apt-get update && apt-get install -y \
     && apt-get clean \
     && apt-get autoclean \
     && apt-get autoremove -y \
-    && rm -rf /var/lib/apt/lists/*\
+    && rm -rf /var/lib/apt/lists/* \
     && echo "${NEW_MAMBA_USER} ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
 # Change user to the non-root user
 USER $MAMBA_USER
@@ -57,68 +57,52 @@ RUN mkdir -p /home/rmguser/Code
 # Change working directory to Code
 WORKDIR /home/rmguser/Code
 
-# Clone the RMG base and database repositories. The pulled branches are only the main branches.
-RUN git clone -b main https://github.com/ReactionMechanismGenerator/RMG-Py.git \
-    && git clone -b main https://github.com/ReactionMechanismGenerator/RMG-database.git
+# ------------------------------------------------------------------ clone & checkout
+WORKDIR /home/rmguser/Code
+RUN git clone --filter=blob:none --no-checkout https://github.com/ReactionMechanismGenerator/RMG-Py.git RMG-Py \
+ && git -C RMG-Py checkout --detach 55464c54d1fa61b531e865682df598d33718597d  \
+ && git clone --filter=blob:none --depth 1 https://github.com/ReactionMechanismGenerator/RMG-database.git RMG-database
 
-# cd into RMG-Py
-WORKDIR /home/rmguser/Code/RMG-Py
 
-# Install RMG-Py and then clean up the micromamba cache
-RUN micromamba create -y -f environment.yml && \
-    micromamba install -n rmg_env -c conda-forge conda && \
-    micromamba clean --all -f -y
 
-# Activate the RMG environment
-ARG MAMBA_DOCKERFILE_ACTIVATE=1
-ENV ENV_NAME=rmg_env
 
-# Set environment variables
-# These need to be set in the Dockerfile so that they are available to the build process
-ENV PATH /opt/conda/envs/rmg_env/bin:$PATH
-ENV PYTHONPATH /home/rmguser/Code/RMG-Py:$PYTHONPATH
-ENV PATH /home/rmguser/Code/RMG-Py:$PATH
+ENV PATH=/opt/conda/envs/rmg_env/bin:/home/rmguser/Code/RMG-Py:$PATH \
+    PYTHONPATH=/home/rmguser/Code/RMG-Py
 
-# Build RMG
-RUN make \
-    && echo "export PYTHONPATH=/home/rmguser/Code/RMG-Py" >> ~/.bashrc \
-    && echo "export PATH=/home/rmguser/Code/RMG-Py:$PATH" >> ~/.bashrc
 
 ENV JULIA_DEPOT_PATH="/home/rmguser/julia-ver/packages"
-ENV JULIA_HISTORY /home/rmguser/repl_history.jl
+ENV JULIA_HISTORY=/home/rmguser/repl_history.jl
 # Since 1.9.0 Julia, the CPU target is set to "native" by default. This is not ideal for a Docker image, so we set it to a list of common CPU targets
 # This avoids the need to compile the Julia packages for the specific CPU architecture of the host machine
 ENV JULIA_CPU_TARGET="x86-64,haswell,skylake,broadwell,znver1,znver2,znver3,cascadelake,icelake-client,cooperlake,generic,native"
-
 # Install RMS
 # The extra arguments are required to install PyCall and RMS in this Dockerfile. Will not work without them.
 # Final command is to compile the RMS during Docker build - This will reduce the time it takes to run RMS for the first time
-RUN touch /opt/conda/envs/rmg_env/condarc-julia.yml
-RUN CONDA_JL_CONDA_EXE=/bin/micromamba julia -e 'ENV["CONDA_JL_CONDA_EXE"]="/opt/conda/envs/rmg_env/bin/conda";using Pkg;Pkg.add(PackageSpec(name="PyCall", rev="master")); Pkg.build("PyCall"); Pkg.add(PackageSpec(name="ReactionMechanismSimulator", rev="main")), using ReactionMechanismSimulator' \
-    && python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()" \
-    && python-jl -c "from pyrms import rms"
-
-RUN python-jl /home/rmguser/Code/RMG-Py/rmg.py /home/rmguser/Code/RMG-Py/examples/rmg/minimal/input.py \
-    # delete the results, preserve input.py
-    && mv /home/rmguser/Code/RMG-Py/examples/rmg/minimal/input.py /home/rmguser/Code/RMG-Py/examples/input.py \
-    && rm -rf /home/rmguser/Code/RMG-Py/examples/rmg/minimal/* \
-    && mv /home/rmguser/Code/RMG-Py/examples/input.py /home/rmguser/Code/RMG-Py/examples/rmg/minimal/input.py
-
-# Add alias to bashrc - rmge to activate the environment
-# These commands are not necessary for the Docker image to run, but they are useful for the user
-RUN echo "alias rmge='micromamba activate rmg_env'" >> ~/.bashrc \
-    && echo "alias arce='micromamba activate arc_env'" >> ~/.bashrc \
-    && echo "alias rmg='python-jl /home/rmguser/Code/RMG-Py/rmg.py input.py'" >> ~/.bashrc \
-    && echo "alias deact='micromamba deactivate'" >> ~/.bashrc \
-    && echo "export rmgpy_path='/home/rmguser/Code/RMG-Py/'" >> ~/.bashrc \
-    && echo "export rmgdb_path='/home/rmguser/Code/RMG-database/'" >> ~/.bashrc \
-    && echo "alias rmgcode='cd \$rmgpy_path'" >> ~/.bashrc \
-    && echo "alias rmgdb='cd \$rmgdb_path'" >> ~/.bashrc \
-    && echo "alias arcode='cd /home/rmguser/Code/ARC'" >> ~/.bashrc \
-    && echo "alias conda='micromamba'" >> ~/.bashrc \
-    && echo "alias mamba='micromamba'" >> ~/.bashrc \
-    && echo "export PYTHONPATH=$PYTHONPATH:/home/rmguser/Code/ARC" >> ~/.bashrc \
-    && echo "export PATH=$PATH:/home/rmguser/Code/ARC" >> ~/.bashrc
+# Julia + PyCall + RMS in rmg_env
+ENV CONDA_JL_CONDA_EXE=/opt/conda/envs/rmg_env/bin/conda
+# ------------------------------------------------------------------ env create
+WORKDIR /home/rmguser/Code/RMG-Py
+RUN micromamba create -y -n rmg_env -f environment.yml \
+    && touch /opt/conda/envs/rmg_env/condarc-julia.yml \
+    && micromamba install -y -n rmg_env -c conda-forge conda \
+    && micromamba clean -a -y \
+    && echo "export PYTHONPATH=/home/rmguser/Code/RMG-Py" >> ~/.bashrc \
+    && echo "export PATH=/home/rmguser/Code/RMG-Py:$PATH" >> ~/.bashrc \
+    &&  micromamba run -n rmg_env make -j"$(nproc)" \
+    && micromamba run -n rmg_env bash -lc "\
+   julia -e 'ENV[\"CONDA_JL_CONDA_EXE\"]=\"${CONDA_JL_CONDA_EXE}\"; using Pkg; \
+             Pkg.add(PackageSpec(name=\"PyCall\", rev=\"master\")); Pkg.build(\"PyCall\"); \
+             Pkg.add(PackageSpec(name=\"ReactionMechanismSimulator\", url=\"https://github.com/ReactionMechanismGenerator/ReactionMechanismSimulator.jl\", rev=\"8dbb07eedebaacf9b9f77081623c572d054b9a6f\")); \
+             using ReactionMechanismSimulator'; \
+   python -c 'import julia, diffeqpy; julia.install(); diffeqpy.install()'; \
+   python-jl -c 'from pyrms import rms' \
+ " 
+
+RUN micromamba run -n rmg_env python-jl /home/rmguser/Code/RMG-Py/rmg.py /home/rmguser/Code/RMG-Py/examples/rmg/minimal/input.py \
+# delete the results, preserve input.py
+&& mv /home/rmguser/Code/RMG-Py/examples/rmg/minimal/input.py /home/rmguser/Code/RMG-Py/examples/input.py \
+&& rm -rf /home/rmguser/Code/RMG-Py/examples/rmg/minimal/* \
+&& mv /home/rmguser/Code/RMG-Py/examples/input.py /home/rmguser/Code/RMG-Py/examples/rmg/minimal/input.py
 
 # Installing ARC
 # Change directory to Code
@@ -132,23 +116,100 @@ WORKDIR /home/rmguser/Code/ARC
 ENV PYTHONPATH="${PYTHONPATH}:/home/rmguser/Code/ARC"
 ENV PYTHONPATH="${PYTHONPATH}:/home/rmguser/Code/AutoTST"
 ENV PYTHONPATH="${PYTHONPATH}:/home/rmguser/Code/TS-GCN"
-ENV PATH /home/rmguser/Code/ARC:$PATH
+ENV PATH=/home/rmguser/Code/ARC:$PATH
 
 # Install ARC Environment
-RUN micromamba create -y -f environment.yml && \
+COPY --chown=rmguser:rmguser ./environment.yml /home/rmguser/Code/ARC/environment.yml
+RUN micromamba create -y -n arc_env -f environment.yml --channel-priority flexible && \
     micromamba clean --all -f -y && \
-    rm -rf /home/rmguser/.cache/yarn \
-    rm -rf /home/rmguser/.cache/pip &&\
-    rm -rf /home/rmguser/.cache/pip && \
-    find -name '*.a' -delete && \
-    find -name '*.pyc' -delete && \
-    find -name '__pycache__' -type d -exec rm -rf '{}' '+' && \
-    find /opt/conda/envs/arc_env/lib/python3.7/site-packages/scipy -name 'tests' -type d -exec rm -rf '{}' '+' && \
-    find /opt/conda/envs/arc_env/lib/python3.7/site-packages/numpy -name 'tests' -type d -exec rm -rf '{}' '+' && \
-    find /opt/conda/envs/arc_env/lib/python3.7/site-packages/pandas -name 'tests' -type d -exec rm -rf '{}' '+' && \
-    find /opt/conda/envs/arc_env/lib/python3.7/site-packages -name '*.pyx' -delete && \
-    rm -rf /opt/conda/envs/arc_env/lib/python3.7/site-packages/uvloop/loop.c && \
-    make clean
+bash -euxo pipefail <<'EOF'
+PYDIR=$(echo /opt/conda/envs/arc_env/lib/python*/site-packages)
+
+# cache
+rm -rf /home/rmguser/.cache/pip /home/rmguser/.cache/yarn
+
+# strip compiled cruft
+find "$PYDIR" -type f \( -name "*.a" -o -name "*.py[co]" \) -delete
+find "$PYDIR" -type d -name "__pycache__" -prune -exec rm -rf {} +
+
+# drop test directories in one traversal
+find "$PYDIR" -type d \( -path "*/scipy/tests" -o -path "*/numpy/tests" -o -path "*/pandas/tests" \) \
+     -prune -exec rm -rf {} +
+
+# remove cython sources
+find "$PYDIR" -name "*.pyx" -delete
+rm -f "$PYDIR/uvloop/loop.c"
+EOF
+
+FROM --platform=linux/amd64 mambaorg/micromamba@sha256:20fb02f2d1160265f7fabaf1601707a902ae65c6dc9e053d305441182450c368 AS arc-stage
+USER root
+ARG NEW_MAMBA_USER=rmguser
+ARG NEW_MAMBA_USER_ID=1000
+ARG NEW_MAMBA_USER_GID=1000
+RUN usermod "--login=${NEW_MAMBA_USER}" "--home=/home/${NEW_MAMBA_USER}" \
+        --move-home "-u ${NEW_MAMBA_USER_ID}" "${MAMBA_USER}" && \
+    groupmod "--new-name=${NEW_MAMBA_USER}" \
+             "-g ${NEW_MAMBA_USER_GID}" "${MAMBA_USER}" && \
+    echo "${NEW_MAMBA_USER}" > "/etc/arg_mamba_user" && \
+    :
+
+# Set the environment variables
+ARG MAMBA_ROOT_PREFIX=/opt/conda
+ENV MAMBA_USER=$NEW_MAMBA_USER
+ENV BASE=$MAMBA_ROOT_PREFIX
+
+# Install system dependencies
+#
+# List of deps and why they are needed:
+#  - make, gcc, g++ for building RMG
+#  - git for downloading RMG respoitories
+#  - wget for downloading conda install script
+#  - libxrender1 required by RDKit
+# Clean up the apt cache to reduce the size of the image
+RUN apt-get update && apt-get install -y \
+    git \
+    gcc \
+    g++ \
+    make \
+    libgomp1\
+    libxrender1 \
+    sudo \
+    nano \
+    && apt-get clean \
+    && apt-get autoclean \
+    && apt-get autoremove -y \
+    && rm -rf /var/lib/apt/lists/* \
+    && echo "${NEW_MAMBA_USER} ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers \
+    && printf '\n# print cheat-sheet once per interactive Bash\nif [[ $- == *i* && $SHLVL -eq 1 ]]; then\n  aliases\nfi\n' \
+        >> /etc/bash.bashrc
+# Change user to the non-root user
+USER $MAMBA_USER
+
+# Make directory for RMG-Py and RMG-database
+RUN mkdir -p /home/rmguser/Code
+
+COPY --from=rmg-stage --chown=rmguser:rmguser /opt/conda /opt/conda
+COPY --from=rmg-stage --chown=rmguser:rmguser /home/rmguser/Code/RMG-Py /home/rmguser/Code/RMG-Py
+COPY --from=rmg-stage --chown=rmguser:rmguser /home/rmguser/Code/RMG-database /home/rmguser/Code/RMG-database
+COPY --from=rmg-stage --chown=rmguser:rmguser /home/rmguser/Code/ARC /home/rmguser/Code/ARC
+
+
+ENV PYTHONPATH="${PYTHONPATH}:/home/rmguser/Code/ARC"
+ENV PYTHONPATH="${PYTHONPATH}:/home/rmguser/Code/AutoTST"
+ENV PYTHONPATH="${PYTHONPATH}:/home/rmguser/Code/TS-GCN"
+ENV PATH=/home/rmguser/Code/ARC:/home/rmguser/Code/RMG-Py:/home/rmguser/Code/RMG-database:$PATH
+ENV PYTHONPATH=/home/rmguser/Code/ARC:/home/rmguser/Code/RMG-Py:/home/rmguser/Code/RMG-database:$PYTHONPATH
+
+ENV JULIA_DEPOT_PATH="/home/rmguser/julia-ver/packages"
+ENV JULIA_HISTORY=/home/rmguser/repl_history.jl
+# Since 1.9.0 Julia, the CPU target is set to "native" by default. This is not ideal for a Docker image, so we set it to a list of common CPU targets
+# This avoids the need to compile the Julia packages for the specific CPU architecture of the host machine
+ENV JULIA_CPU_TARGET="x86-64,haswell,skylake,broadwell,znver1,znver2,znver3,cascadelake,icelake-client,cooperlake,generic"
+# Install RMS
+# The extra arguments are required to install PyCall and RMS in this Dockerfile. Will not work without them.
+# Final command is to compile the RMS during Docker build - This will reduce the time it takes to run RMS for the first time
+# Julia + PyCall + RMS in rmg_env
+ENV CONDA_JL_CONDA_EXE=/opt/conda/envs/rmg_env/bin/conda
 
 WORKDIR /home/rmguser/
 
@@ -157,15 +218,25 @@ RUN mkdir -p /home/rmguser/.arc && \
     cp /home/rmguser/Code/ARC/arc/settings/submit.py /home/rmguser/.arc/submit.py
 
 # Copy alias_print.sh and entrywrapper.sh to the container
-COPY --chown=rmguser:rmguser ./dockerfiles/alias_print.sh /home/rmguser/alias_print.sh
-COPY --chown=rmguser:rmguser ./dockerfiles/entrywrapper.sh /home/rmguser/entrywrapper.sh
-
-# Make the scripts executable
-RUN chmod +x /home/rmguser/alias_print.sh \
-    && chmod +x /home/rmguser/entrywrapper.sh
+# Copy your login‐wide aliases into /etc/profile.d
+COPY --chown=rmguser:rmguser dockerfiles/aliases.sh /etc/profile.d/99-rmg-aliases.sh
+
+# Copy the cheat‐sheet and entrypoint
+COPY --chown=rmguser:rmguser dockerfiles/aliases_print.sh /usr/local/bin/aliases
+COPY --chown=rmguser:rmguser dockerfiles/entrywrapper.sh  /home/rmguser/entrywrapper.sh
+
+# Fix permissions & make the scripts executable & ensure rms is run once
+RUN chmod 644 /etc/profile.d/99-rmg-aliases.sh \
+ && chmod +x /home/rmguser/entrywrapper.sh \
+ && chmod +x /usr/local/bin/aliases \
+    && micromamba run -n rmg_env python-jl /home/rmguser/Code/RMG-Py/rmg.py /home/rmguser/Code/RMG-Py/examples/rmg/minimal/input.py \
+    # delete the results, preserve input.py
+    && mv /home/rmguser/Code/RMG-Py/examples/rmg/minimal/input.py /home/rmguser/Code/RMG-Py/examples/input.py \
+    && rm -rf /home/rmguser/Code/RMG-Py/examples/rmg/minimal/* \
+    && mv /home/rmguser/Code/RMG-Py/examples/input.py /home/rmguser/Code/RMG-Py/examples/rmg/minimal/input.py
 
-# Set the wrapper script as the entrypoint
-ENTRYPOINT ["/home/rmguser/entrywrapper.sh"]
+# Use a login shell so /etc/profile and /etc/profile.d/* are sourced automatically
+ENTRYPOINT ["bash","-l","/home/rmguser/entrywrapper.sh"]
 
 # Activate the ARC environment
 ARG MAMBA_DOCKERFILE_ACTIVATE=1
diff --git a/devtools/xtb_environment.yml b/devtools/xtb_environment.yml
index 55f712a8ce..dc74c2c433 100644
--- a/devtools/xtb_environment.yml
+++ b/devtools/xtb_environment.yml
@@ -5,4 +5,4 @@ dependencies:
   - python=3.7
   - xtb=6.3.3
   - pyyaml
-  
\ No newline at end of file
+  - libgfortran=14.2.0
diff --git a/dockerfiles/alias_print.sh b/dockerfiles/alias_print.sh
deleted file mode 100755
index cb51484cea..0000000000
--- a/dockerfiles/alias_print.sh
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/bin/bash
-
-# Source .bashrc to load aliases
-if [ -f ~/.bashrc ]; then
-    source ~/.bashrc
-fi
-
-# Print the aliases
-echo "Alias List with Descriptions:"
-echo ""
-echo "1. rmge ='micromamba activate rmg_env'"
-echo "   - Activates the 'rmg_env' environment using Conda."
-echo ""
-echo "2. arce ='micromamba activate arc_env'"
-echo "   - Activates the 'arc_env' environment using Conda."
-echo ""
-echo "3. rmg ='python-jl /home/rmguser/Code/RMG-Py/rmg.py input.py'"
-echo "   - Runs the RMG program with 'input.py' using Python in the Julia environment."
-echo ""
-echo "4. deact ='micromamba deactivate'"
-echo "   - Deactivates the current Micromamba environment."
-echo ""
-echo "5. rmgcode='cd /home/rmguser/Code/RMG-Py/'"
-echo "   - Changes the current directory to the RMG-Py code directory."
-echo ""
-echo "6. rmgdb ='cd /home/rmguser/Code/RMG-database/"
-echo "   - Changes the current directory to the RMG database directory."
-echo ""
-echo "7. arcode ='cd /home/rmguser/Code/ARC'"
-echo "   - Changes the current directory to the ARC code directory."
-echo ""
-
-# Execute the command specified as CMD in Dockerfile, or the command passed to docker run
-exec "$@"
diff --git a/dockerfiles/aliases.sh b/dockerfiles/aliases.sh
new file mode 100644
index 0000000000..7e56be1fb7
--- /dev/null
+++ b/dockerfiles/aliases.sh
@@ -0,0 +1,28 @@
+# personalised shortcuts – sourced for every login shell
+alias rc='source ~/.bashrc'
+alias rce='nano ~/.bashrc'
+alias erc='nano ~/.bashrc'
+
+# micromamba drop-ins
+alias mamba='micromamba'
+alias conda='micromamba'
+alias deact='micromamba deactivate'
+
+# env activators
+alias rmge='micromamba activate rmg_env'
+alias arce='micromamba activate arc_env'
+
+# code roots (set once at image build)
+export rmgpy_path=/home/rmguser/Code/RMG-Py
+export rmgdb_path=/home/rmguser/Code/RMG-database
+export arc_path=/home/rmguser/Code/ARC
+
+alias rmgcode='cd "$rmgpy_path"'
+alias dbcode='cd "$rmgdb_path"'
+alias arcode='cd "$arc_path"'
+
+# job wrappers
+alias rmg='python-jl "$rmgpy_path/rmg.py" input.py  > >(tee -a stdout.log) 2> >(tee -a stderr.log >&2)'
+alias arkane='python "$rmgpy_path/Arkane.py" input.py  > >(tee -a stdout.log) 2> >(tee -a stderr.log >&2)'
+alias arc='python "$arc_path/ARC.py" input.yml  > >(tee -a stdout.log) 2> >(tee -a stderr.log >&2)'
+alias arcrestart='python "$arc_path/ARC.py" restart.yml > >(tee -a stdout.log) 2> >(tee -a stderr.log >&2)'
diff --git a/dockerfiles/aliases_print.sh b/dockerfiles/aliases_print.sh
new file mode 100644
index 0000000000..44ed7eb6aa
--- /dev/null
+++ b/dockerfiles/aliases_print.sh
@@ -0,0 +1,31 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# ensure the aliases defined in /etc/profile.d/ are loaded
+# (interactive login shells source them automatically, but
+# non-login shells like `docker exec … bash` do not)
+shopt -q login_shell || source /etc/profile
+
+cat <<'EOF'
+╭─────────────────────────────────────────────────────────────╮
+│  Built-in aliases & helpers                                │
+╰─────────────────────────────────────────────────────────────╯
+
+‣ Environment switches
+    rmge        →  micromamba activate rmg_env
+    arce        →  micromamba activate arc_env
+    deact       →  micromamba deactivate
+
+‣ Jump to source trees
+    rmgcode     →  cd $rmgpy_path
+    dbcode      →  cd $rmgdb_path
+    arcode      →  cd $arc_path
+
+‣ One-liner runners
+    rmg         →  python-jl $rmgpy_path/rmg.py    input.py
+    arkane      →  python    $rmgpy_path/Arkane.py input.py
+    arc         →  python    $arc_path/ARC.py      input.yml
+    arcrestart  →  python    $arc_path/ARC.py      restart.yml
+
+Type  aliases   again at any time to reopen this cheat-sheet.
+EOF
diff --git a/dockerfiles/entrywrapper.sh b/dockerfiles/entrywrapper.sh
index ce947f7158..388315afc2 100644
--- a/dockerfiles/entrywrapper.sh
+++ b/dockerfiles/entrywrapper.sh
@@ -1,61 +1,34 @@
-#!/bin/bash
+#!/usr/bin/env bash
+set -euo pipefail
 
-# Function to initialize Micromamba
-initialize_micromamba() {
-    eval "$(micromamba shell hook --shell bash)"
-}
+# 1) Micromamba setup (for both interactive & non-interactive)
+eval "$(micromamba shell hook --shell bash)"
 
-# Function to check and adjust permissions for mounted directories
-# Excludes directories within /opt
-check_and_adjust_permissions() {
-    for dir in /home/rmguser/*; do
-        # Check if it's a directory and ensure it's not within /opt
-        if [ -d "$dir" ] && [[ $dir != /opt/* ]]; then
-            # Adjust permissions for the directory
-            chmod -R 777 "$dir"
-        fi
-    done
-}
-
-# Function to run for interactive mode
-run_interactive() {
-    check_and_adjust_permissions
-    echo "Container started in interactive mode"
-    
-    /home/rmguser/alias_print.sh
-    
-    /bin/bash
-}
-
-# Function to run for non-interactive mode
-run_non_interactive() {
-    check_and_adjust_permissions
-    echo "Container started in non-interactive mode"
-    initialize_micromamba
-
-    case "$1" in
-        rmg)
-            # Activate rmg_env and run RMG with python-jl
-            echo "Running with RMG environment..."
-            micromamba activate rmg_env
-            python-jl /home/rmguser/Code/RMG-Py/rmg.py "$2"
-            ;;
-        arc)
-            # Activate arc_env and run ARC
-            echo "Running with ARC environment..."
-            micromamba activate arc_env
-            python /home/rmguser/Code/ARC/ARC.py "$2"
-            ;;
-        *)
-            echo "Invalid option. Please specify 'rmg' or 'arc' as the first argument."
-            exit 1
-            ;;
-    esac
-}
+# 1.1) Ensure the Code directory is owned by rmguser
+if [ ! -O /home/rmguser/Code ]; then
+  chown -R rmguser:rmguser /home/rmguser/Code
+fi
 
-# Determine the run mode based on CONTAINER_MODE environment variable or terminal attachment
-if [ "$CONTAINER_MODE" = "interactive" ] || ([ -z "$CONTAINER_MODE" ] && [ -t 0 ] && [ -t 1 ]); then
-    run_interactive
-else
-    run_non_interactive "$@"
+# 2) Interactive mode: login shells or docker exec … bash
+if [ -t 0 ] && [ -t 1 ]; then
+#   # Show the aliases cheat-sheet
+#   /home/rmguser/.aliases_print.sh
+  # Drop into an interactive Bash
+  exec /bin/bash -l
 fi
+
+# 3) Non-interactive command mode: rmg or arc
+case "${1:-}" in
+  rmg)
+    micromamba activate rmg_env
+    exec python-jl /home/rmguser/Code/RMG-Py/rmg.py "${2:-input.py}"
+    ;;
+  arc)
+    micromamba activate arc_env
+    exec python /home/rmguser/Code/ARC/ARC.py "${2:-input.yml}"
+    ;;
+  *)
+    echo "Usage: <rmg|arc> [input-file]" >&2
+    exit 1
+    ;;
+esac
diff --git a/environment.yml b/environment.yml
index cdad14ac3a..d9377c0899 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,61 +1,72 @@
 name: arc_env
 channels:
-  - defaults
-  - rmg
-  - conda-forge
-  - cantera
-  - anaconda
+  - rmg          # RMG-specific wheels
+  - conda-forge  # modern science stack
+  - cantera      # cantera 2.6 build
+  - defaults     # only for legacy libs like libboost 1.67
+
 dependencies:
-  - cairo
-  - cairocffi
-  - cantera::cantera=2.6
-  - conda-forge::cclib >=1.7.0
+  # ——— hard pins ————————————————————————————————
+  - python=3.7.*
+  - numpy=1.20.1
+
+  # ——— chemistry / RMG stack ————————————————
   - rmg::chemprop
-  - coolprop
-  - coverage
-  - cython >=0.25.2
-  - ffmpeg
-  - rmg::gprof2dot
-  - graphviz
-  - h5py
-  - jinja2
-  - jupyter
+  - rmg::pydas>=1.0.2
+  - rmg::pydqed>=1.0.1
+  - rmg::pyrdl
   - rmg::lpsolve55
-  - markupsafe
-  - matplotlib >=1.5
-  - conda-forge::mopac
-  - mpmath
-  - rmg::muq2
-  - networkx
   - rmg::numdifftools
-  - numpy==1.20.1
-  - conda-forge::openbabel >= 3
+  - rmg::quantities
+  - rmg::muq2
+
+  # rdkit from conda-forge (links to boost-cpp ≥1.70, no missing libboost)
+  - conda-forge::rdkit>=2020.03.3.0
+
+  # ——— core numerics / plotting ——————————————
+  - scipy
   - pandas
+  - scikit-learn
+  - matplotlib>=1.5
+  - h5py
+  - networkx
+  - cython>=0.25.2
   - psutil
-  - rmg::pydas >=1.0.2
+  - mpmath
   - pydot
-  - rmg::pydqed >=1.0.1
-  - pymongo
   - pyparsing
-  - rmg::pyrdl
-  - python >=3.7
   - pyyaml
-  - rmg::quantities
-  - rmg::rdkit >=2020.03.3.0
-  - scikit-learn
-  - scipy
-  - connie::symmetry
+
+  # ——— thermo / quantum extras ——————————————
+  - cantera::cantera=2.6
+  - conda-forge::openbabel=3.*
+  - conda-forge::cclib>=1.7.0
+  - conda-forge::mopac
+  - conda-forge::qcelemental
+  - conda-forge::ase=3.22.1
+  - coolprop
+
+  # ——— utilities ————————————————————————————————
+  - cairo
+  - cairocffi
+  - ffmpeg
+  - graphviz
   - xlrd
   - xlwt
-  - anaconda::sphinx_rtd_theme
-  - anaconda::paramiko >=2.6.0
-  - conda-forge::py3dmol >= 0.8.0
-  - conda-forge::ase==3.22.1
-  - anaconda::ipython
-  - anaconda::sphinx
-  - anaconda::sphinxcontrib-jsmath
-  - conda-forge::qcelemental
-  - mako
+  - jinja2
+  - markupsafe
+  - paramiko=2.6.*
+  - connie::symmetry
   - pytables
-  - anaconda::pytest
+
+  # ——— docs / notebooks / tests (optional) ———————
+  - jupyter=1.0.*
+  - sphinx
+  - sphinx_rtd_theme
+  - sphinxcontrib-jsmath
+  - mako=1.2.3
+  - pytest
   - conda-forge::pytest-cov
+  - conda-forge::py3dmol>=0.8.0
+  - coverage
+  - ipython