diff --git a/.devcontainer/vscode-init/02-download-extensions.sh b/.devcontainer/vscode-init/02-download-extensions.sh
index 38e7b83..134f6f4 100755
--- a/.devcontainer/vscode-init/02-download-extensions.sh
+++ b/.devcontainer/vscode-init/02-download-extensions.sh
@@ -10,7 +10,7 @@ set -e
 # of the extension and its functionality gets inherited by devcontainers.
 
 EXTENSIONS_FILE="extensions-to-download.txt"
-DOWNLOAD_DIR="/opt/vscode-extensions"
+DOWNLOAD_DIR=${1:-"/opt/vscode-extensions"}
 SUCCESSFUL_DOWNLOADS=()
 
 mkdir -p "${DOWNLOAD_DIR}"
diff --git a/.devcontainer/vscode-init/extensions-to-install.txt b/.devcontainer/vscode-init/extensions-to-install.txt
index 9fb91ff..ad05bce 100644
--- a/.devcontainer/vscode-init/extensions-to-install.txt
+++ b/.devcontainer/vscode-init/extensions-to-install.txt
@@ -2,10 +2,8 @@
 # These extensions will be enabled for all users of the devcontainer.
 # One extension ID per line.
 charliermarsh.ruff
-Continue.continue --pre-release
 DavidAnson.vscode-markdownlint
 eamodio.gitlens
-# The marimo extension has been removed from the marketplace whilst it is being rewritten.
 marimo-team.vscode-marimo
 mechatroner.rainbow-csv
 ms-ossdata.vscode-pgsql --pre-release
@@ -15,5 +13,4 @@ ms-toolsai.jupyter
 #openai.chatgpt
 qwenlm.qwen-code-vscode-ide-companion
 REditorSupport.r
-REditorSupport.r-syntax
 yzhang.markdown-all-in-one
\ No newline at end of file
diff --git a/Dockerfile b/Dockerfile
index 4af3251..8f04168 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -6,26 +6,21 @@ ARG VSCODE_COMMIT=bf9252a2fb45be6893dd8870c0bf37e2e1766d61
 
 ENV VSCODE_COMMIT=${VSCODE_COMMIT}
 
-# Copy and run VS Code installation files
-COPY .devcontainer/vscode-init /opt/vscode-init
-
-# Copy Qwen settings
-COPY .devcontainer/qwen-settings.json /root/.qwen/settings.json
-
-# Copy Codex config
-COPY .devcontainer/codex-config.toml /root/.codex/config.toml
-
-# Copy Continue Dev config
-COPY .devcontainer/continue-config.yaml /root/.continue/config.yaml
-COPY .devcontainer/continue.env /root/.continue/.env
-
-# Copy scripts folder to /opt/scripts (accessible at runtime)
-COPY scripts /opt/scripts
-
-RUN cd /opt/vscode-init \ 
-    && ./00-install-vscode-server.sh ${VSCODE_COMMIT} \
-    && ./01-install-extensions.sh ${VSCODE_COMMIT} \
-    && ./02-download-extensions.sh
+# Copy custom scripts and installation files
+COPY .devcontainer /opt/.devcontainer
+
+# Copy devcontainerctl folder to /opt/devcontainerctl (accessible at runtime)
+COPY devcontainerctl /opt/devcontainerctl
+
+# Run VS Code installation files & copy configurations
+RUN cd /opt/.devcontainer/vscode-init \ 
+    && /opt/.devcontainer/vscode-init/00-install-vscode-server.sh ${VSCODE_COMMIT} \
+    && /opt/.devcontainer/vscode-init/01-install-extensions.sh ${VSCODE_COMMIT} \
+    && /opt/.devcontainer/vscode-init/02-download-extensions.sh /opt/vscode-extensions \
+    && mkdir -p /root/.qwen && cp /opt/.devcontainer/qwen-settings.json /root/.qwen/settings.json \
+    && mkdir -p /root/.codex && cp /opt/.devcontainer/codex-config.toml /root/.codex/config.toml \
+    && mkdir -p /root/.continue && cp /opt/.devcontainer/continue-config.yaml /root/.continue/config.yaml \
+    && cp /opt/.devcontainer/continue.env /root/.continue/.env
 
 WORKDIR /workspace
 
diff --git a/README.md b/README.md
index 9d74dfc..6769a2d 100644
--- a/README.md
+++ b/README.md
@@ -66,10 +66,10 @@ ces-pull a a ghcr.io/smartdatafoundry/devcontainer:latest
 # 2. Extract the setup scripts
 podman run --rm -v $HOME:$HOME -w $HOME \
   ghcr.io/smartdatafoundry/devcontainer:latest \
-  cp -r /opt/scripts $HOME/devcontainer-scripts
+  cp -r /opt/devcontainerctl $HOME/devcontainerctl
 
 # 3. Run the setup script (one-time setup)
-cd $HOME/devcontainer-scripts
+cd $HOME/devcontainerctl
 ./setup.sh
 
 # 4. Start your devcontainer
@@ -106,7 +106,7 @@ For detailed manual setup instructions, see the **[SDF TRE Setup Guide](docs/SDF
 |-------|-----------|
 | SDF TRE usage | [`docs/SDF_TRE_SETUP.md`](docs/SDF_TRE_SETUP.md) |
 | Full container internals | [`docs/DEVCONTAINER.md`](docs/DEVCONTAINER.md) |
-| Setup scripts | [`scripts/`](scripts/) directory |
+| Setup scripts | [`devcontainerctl/`](devcontainerctl/) directory |
 | Reusable publish workflow | [`docs/BUILD_PUBLISH_CONTAINER.md`](docs/BUILD_PUBLISH_CONTAINER.md) |
 | Dev Container Specification | https://containers.dev |
 
@@ -119,7 +119,7 @@ For detailed manual setup instructions, see the **[SDF TRE Setup Guide](docs/SDF
 - **Shell**: Zsh with Oh My Zsh (via common-utils feature)
 - **Quarto**: Document publishing platform (latest version)
 - **Marimo**: Markdown presentation tool, alternative to Jupyter Notebooks
-- **User Setup Scripts**: Automated deployment and management tools ([`scripts/`](scripts/))
+- **User Setup Scripts**: Automated deployment and management tools ([`devcontainerctl/`](devcontainerctl/))
 - **VS Code Extensions (curated)**:
   - Continue (AI assistant)
   - Black (Python formatting)
diff --git a/scripts/devcontainerctl b/devcontainerctl/devcontainerctl
similarity index 100%
rename from scripts/devcontainerctl
rename to devcontainerctl/devcontainerctl
diff --git a/scripts/setup.sh b/devcontainerctl/setup.sh
similarity index 70%
rename from scripts/setup.sh
rename to devcontainerctl/setup.sh
index 9319da2..bf757b9 100644
--- a/scripts/setup.sh
+++ b/devcontainerctl/setup.sh
@@ -11,11 +11,12 @@ NC='\033[0m' # No Color
 echo -e "${GREEN}DevContainer Setup Script${NC}"
 echo "================================"
 
-# Define paths
+# Define files & paths
 SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
 SCRIPT_SOURCE="$SCRIPT_DIR/devcontainerctl"
 SYMLINK_TARGET="$HOME/bin/devcontainerctl"
 CRON_COMMAND="0 8 * * * $SYMLINK_TARGET sync"
+EXTENSION_FILE="/safe_data/shared/vscode-extensions/ms-vscode-remote.remote-containers.vsix"
 
 # Check if source script exists
 if [ ! -f "$SCRIPT_SOURCE" ]; then
@@ -23,6 +24,18 @@ if [ ! -f "$SCRIPT_SOURCE" ]; then
     exit 1
 fi
 
+# Install VS Code remote containers extensions if code command is available
+if command -v code >/dev/null 2>&1; then
+    echo -e "${YELLOW}Installing VS Code remote containers extension...${NC}"
+    code --install-extension $EXTENSION_FILE || {
+        echo -e "${RED}Failed to install remote containers extension${NC}"
+        exit 1
+    }
+else
+    echo -e "${RED}VS Code command 'code' not found. Skipping extension installation.${NC}"
+    exit 1
+fi
+
 # Create ~/bin directory if it doesn't exist
 if [ ! -d "$HOME/bin" ]; then
     echo -e "${YELLOW}Creating $HOME/bin directory...${NC}"
@@ -32,7 +45,7 @@ fi
 # Create symlink
 if [ -L "$SYMLINK_TARGET" ]; then
     echo -e "${YELLOW}Symlink already exists at $SYMLINK_TARGET${NC}"
-    echo "Removing old symlink..."
+    echo -e "${YELLOW}Removing old symlink...${NC}"
     rm "$SYMLINK_TARGET"
 fi
 
@@ -42,7 +55,7 @@ ln -s "$SCRIPT_SOURCE" "$SYMLINK_TARGET"
 # Make sure the source script is executable
 if [ ! -x "$SCRIPT_SOURCE" ]; then
     echo -e "${YELLOW}Warning: $SCRIPT_SOURCE is not executable${NC}"
-    echo "You may need to run: sudo chmod +x $SCRIPT_SOURCE"
+    echo -e "${YELLOW}You may need to run: sudo chmod +x $SCRIPT_SOURCE${NC}"
 fi
 
 # Add ~/bin to PATH if not already present
@@ -75,9 +88,9 @@ echo ""
 echo "================================"
 echo -e "${GREEN}Setup Complete!${NC}"
 echo ""
-echo "Verification:"
-echo "  Symlink: $(ls -la $SYMLINK_TARGET 2>/dev/null || echo 'Not found')"
-echo "  Cron job:"
-crontab -l | grep "devcontainerctl sync" || echo "  Not found"
+echo -e "${GREEN}Verification:${NC}"
+echo -e "${GREEN}  Symlink: $(ls -la $SYMLINK_TARGET 2>/dev/null || echo 'Not found')${NC}"
+echo -e "${GREEN}  Cron job:${NC}"
+crontab -l | grep "devcontainerctl sync" || echo -e "${GREEN}  Not found${NC}"
 echo ""
 echo -e "${YELLOW}Note: You may need to restart your shell or run 'source ~/.bashrc'${NC}"
\ No newline at end of file
diff --git a/docs/DEVCONTAINER.md b/docs/DEVCONTAINER.md
index 71df145..34ce605 100644
--- a/docs/DEVCONTAINER.md
+++ b/docs/DEVCONTAINER.md
@@ -75,13 +75,13 @@ This dev container includes:
 * **Marimo**: Alternative interactive notebook/presentation tool
 * **VS Code Server**: Pre-installed (pin via tag families)
 * **VS Code Extensions**: Curated list (see [`.devcontainer/vscode-init/extensions-to-install.txt`](.devcontainer/vscode-init/extensions-to-install.txt))
-* **User Setup Scripts**: Automated deployment and management tools (at `/opt/scripts/` in container)
+* **User Setup Scripts**: Automated deployment and management tools (at `/opt/devcontainerctl/` in container)
 
 ### User Setup Scripts
 
-The container includes scripts in [`/opt/scripts/`](../scripts/) to simplify deployment and management:
+The container includes scripts in [`/opt/devcontainerctl/`](../devcontainerctl/) to simplify deployment and management:
 
-#### [`scripts/devcontainerctl`](scripts/devcontainerctl)
+#### [`devcontainerctl/devcontainerctl`](../devcontainerctl/devcontainerctl)
 A comprehensive container lifecycle management script that provides:
 
 **Features:**
@@ -112,7 +112,7 @@ devcontainerctl stop                # Stop container
 devcontainerctl remove              # Remove container
 ```
 
-#### [`scripts/setup.sh`](scripts/setup.sh)
+#### [`devcontainerctl/setup.sh`](../devcontainerctl/setup.sh)
 One-time setup script that configures your environment:
 
 **What it does:**
@@ -120,16 +120,17 @@ One-time setup script that configures your environment:
 - Creates symlink to `devcontainerctl` in `~/bin`
 - Adds `~/bin` to PATH in `~/.bashrc`
 - Configures daily cron job (8:00 AM) to sync images using `devcontainerctl sync`
+- Installs VS Code remote extensions for devcontainer enablement
 
 **Usage:**
 ```bash
 # Extract scripts from container first
 podman run --rm -v $HOME:$HOME -w $HOME \
   ghcr.io/smartdatafoundry/devcontainer:latest \
-  cp -r /opt/scripts $HOME/devcontainer-scripts
+  cp -r /opt/devcontainerctl $HOME/devcontainerctl
 
 # Run setup
-cd $HOME/devcontainer-scripts
+cd $HOME/devcontainerctl
 ./setup.sh
 ```
 
@@ -186,7 +187,7 @@ This keeps maintenance simple: update the default by editing a single line in [`
 │   ├── build-devcontainer.yml     # Dev container build workflow
 │   ├── build-publish-container.yml # Container publishing workflow
 │   └── update-vscode.yml          # VS Code version update workflow
-├── scripts/                       # User deployment scripts
+├── devcontainerctl/               # User deployment scripts
 │   ├── devcontainerctl            # Container management script
 │   └── setup.sh                   # One-time setup script
 ├── assets/                        # Documentation assets
diff --git a/docs/SDF_TRE_SETUP.md b/docs/SDF_TRE_SETUP.md
index 4793689..b2d77ea 100644
--- a/docs/SDF_TRE_SETUP.md
+++ b/docs/SDF_TRE_SETUP.md
@@ -15,10 +15,10 @@ ces-pull a a ghcr.io/smartdatafoundry/devcontainer:latest
 # 2. Extract the setup scripts
 podman run --rm -v $HOME:$HOME -w $HOME \
   ghcr.io/smartdatafoundry/devcontainer:latest \
-  cp -r /opt/scripts $HOME/devcontainer-scripts
+  cp -r /opt/devcontainerctl $HOME/devcontainerctl
 
 # 3. Run the one-time setup
-cd $HOME/devcontainer-scripts
+cd $HOME/devcontainerctl
 ./setup.sh
 
 # 4. Start your devcontainer
@@ -53,7 +53,7 @@ The devcontainer includes scripts that automate deployment and management in the
 After extracting the scripts (see Quick Start above), run the setup script:
 
 ```bash
-cd $HOME/devcontainer-scripts
+cd $HOME/devcontainerctl
 ./setup.sh
 ```