diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index 7760128..436d7e2 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -7,8 +7,8 @@ ARG VSCODE_COMMIT
 COPY ./vscode-init /opt/vscode-init
 RUN cd /opt/vscode-init \ 
     && ./00-install-vscode-server.sh ${VSCODE_COMMIT} \
-    && ./01-install-vscode-extensions.sh ${VSCODE_COMMIT} \
-    && ./02-download-container-tools-extension.sh
+    && ./01-install-extensions.sh ${VSCODE_COMMIT} \
+    && ./02-download-extensions.sh
 
 WORKDIR /workspace
 
diff --git a/.devcontainer/vscode-init/01-install-vscode-extensions.sh b/.devcontainer/vscode-init/01-install-extensions.sh
similarity index 97%
rename from .devcontainer/vscode-init/01-install-vscode-extensions.sh
rename to .devcontainer/vscode-init/01-install-extensions.sh
index 2bbbbd5..4ac30a2 100755
--- a/.devcontainer/vscode-init/01-install-vscode-extensions.sh
+++ b/.devcontainer/vscode-init/01-install-extensions.sh
@@ -6,7 +6,7 @@ set -e
 
 VSCODE_COMMIT=${1:-"7adae6a56e34cb64d08899664b814cf620465925"}
 VSCODE_SERVER_HOME="/root/.vscode-server/bin/${VSCODE_COMMIT}"
-EXTENSIONS_FILE="vscode-extensions.txt"
+EXTENSIONS_FILE="extensions-to-install.txt"
 
 # Check if VS Code server is installed
 if [ ! -f "${VSCODE_SERVER_HOME}/bin/code-server" ]; then
diff --git a/.devcontainer/vscode-init/02-download-container-tools-extension.sh b/.devcontainer/vscode-init/02-download-container-tools-extension.sh
deleted file mode 100755
index 0cde65b..0000000
--- a/.devcontainer/vscode-init/02-download-container-tools-extension.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/bin/env bash
-set -e
-
-# Container Tools Extension download script
-# This script downloads the compatible Container Tools extension (ms-vscode-remote.remote-containers) 
-# VSIX file for the specified VS Code commit to /opt/
-
-DOWNLOAD_DIR="/opt"
-EXTENSION_PUBLISHER="ms-vscode-remote"
-EXTENSION_NAME="remote-containers"
-
-EXTENSION_ID="${EXTENSION_PUBLISHER}.${EXTENSION_NAME}"
-EXTENSION_FILEPATH="${DOWNLOAD_DIR}/${EXTENSION_PUBLISHER}.${EXTENSION_NAME}.vsix"
-DOWNLOAD_URL="https://${EXTENSION_PUBLISHER}.gallery.vsassets.io/_apis/public/gallery/publisher/${EXTENSION_PUBLISHER}/extension/${EXTENSION_NAME}/latest/assetbyname/Microsoft.VisualStudio.Services.VSIXPackage"
-
-# Download the extension VSIX file
-echo "Downloading ${EXTENSION_ID} extension..."
-echo "Target directory: ${DOWNLOAD_DIR}"
-echo "Download URL: ${DOWNLOAD_URL}"
-curl -sSL -o "${EXTENSION_FILEPATH}" "${DOWNLOAD_URL}"
-
-# Verify the download
-if [ -f "${EXTENSION_FILEPATH}" ]; then
-    echo "Container Tools extension downloaded successfully to ${EXTENSION_FILEPATH}"
-    
-    # Display file information
-    echo "File size: $(du -h "${EXTENSION_FILEPATH}" | cut -f1)"
-else
-    echo "Error: Failed to download Container Tools extension"
-    # exit 1
-fi
-
-echo "Container Tools extension download completed successfully"
diff --git a/.devcontainer/vscode-init/02-download-extensions.sh b/.devcontainer/vscode-init/02-download-extensions.sh
new file mode 100755
index 0000000..06c28d2
--- /dev/null
+++ b/.devcontainer/vscode-init/02-download-extensions.sh
@@ -0,0 +1,87 @@
+#!/bin/env bash
+set -e
+
+# Some extensions are for the system VS Code, e.g. Dev Containers.
+# Because installed extensions are enabled by default, and an extension
+# like e.g. VS Code Vim would be disruptive to most users, we can
+# download them instead. Then it is up to the user to extract and
+# install the extension into their system VS Code in the TRE.
+# In some cases, such as for VS Code Vim, the system VS Code install
+# of the extension and its functionality gets inherited by devcontainers.
+
+EXTENSIONS_FILE="extensions-to-download.txt"
+DOWNLOAD_DIR="/opt"
+SUCCESSFUL_DOWNLOADS=()
+
+if [ ! -f "${EXTENSIONS_FILE}" ]; then
+    echo "Error: Extensions file not found at ${EXTENSIONS_FILE}"
+    exit 1
+fi
+
+echo ""
+echo "Reading extensions from: ${EXTENSIONS_FILE}"
+echo "Target directory: ${DOWNLOAD_DIR}"
+echo ""
+
+download_extension() {
+    local extension_id="$1"
+
+    # Skip empty lines and comments
+    if [[ -z "$extension_id" || "$extension_id" =~ ^[[:space:]]*# ]]; then
+        return 0
+    fi
+    
+    # Example of valid ID: publisher-name.extension-name
+    if [[ "$extension_id" != *.* ]]; then
+        echo "Invalid extension ID format '$extension_id' - check for typos"
+        exit 1
+    fi
+    
+    local publisher="${extension_id%.*}"
+    local extension_name="${extension_id#*.}"
+    
+    local extension_filepath="${DOWNLOAD_DIR}/${extension_id}.vsix"
+    local download_url="https://${publisher}.gallery.vsassets.io/_apis/public/gallery/publisher/${publisher}/extension/${extension_name}/latest/assetbyname/Microsoft.VisualStudio.Services.VSIXPackage"
+    
+    echo "Downloading ${extension_id}..."
+    
+    if curl -sSL -o "${extension_filepath}" "${download_url}"; then
+        if [ -f "${extension_filepath}" ] && [ -s "${extension_filepath}" ]; then
+            if [ "$(cat "${extension_filepath}" | jq -r '.typeKey' 2>/dev/null)" = "ExtensionDoesNotExistException" ]; then
+                echo "  ✗ Download failed: $extension_id does not exist"
+                echo "Response from Microsoft:"
+                cat "${extension_filepath}" | jq .
+                exit 1
+            fi
+        fi
+        
+        if [ -f "${extension_filepath}" ] && [ -s "${extension_filepath}" ]; then
+            echo "  ✓ Downloaded successfully ($(du -h "${extension_filepath}" | cut -f1))"
+            SUCCESSFUL_DOWNLOADS+=("$extension_id")
+        else
+            echo "  ✗ Download failed - file is empty or missing"
+            [ -f "${extension_filepath}" ] && rm -f "${extension_filepath}"
+            exit 1
+        fi
+    else
+        echo "  ✗ Download failed - curl error"
+        [ -f "${extension_filepath}" ] && rm -f "${extension_filepath}"
+        exit 1
+    fi
+}
+
+# Read and process each extension
+while IFS= read -r extension_id || [ -n "$extension_id" ]; do
+    # Remove leading/trailing whitespace
+    extension_id=$(echo "$extension_id" | sed 's/^[[:space:]]*//;s/[[:space:]]*$//')
+    download_extension "$extension_id"
+done < "${EXTENSIONS_FILE}"
+
+if [ ${#SUCCESSFUL_DOWNLOADS[@]} -eq 0 ]; then
+    echo "No extensions found in ${EXTENSIONS_FILE}."
+    echo ""
+else
+    echo "All extensions downloaded successfully:"
+    printf "  ✓ %s\n" "${SUCCESSFUL_DOWNLOADS[@]}"
+    echo ""
+fi
diff --git a/.devcontainer/vscode-init/extensions-to-download.txt b/.devcontainer/vscode-init/extensions-to-download.txt
new file mode 100644
index 0000000..ae18db9
--- /dev/null
+++ b/.devcontainer/vscode-init/extensions-to-download.txt
@@ -0,0 +1,6 @@
+# VS Code extensions list for downloading
+# These extensions are to be extracted from the image and installed
+# into the user's VS Code. They will not be available in the devcontainer.
+# One extension ID per line.
+ms-vscode-remote.remote-containers
+vscodevim.vim
\ No newline at end of file
diff --git a/.devcontainer/vscode-init/extensions-to-install.txt b/.devcontainer/vscode-init/extensions-to-install.txt
new file mode 100644
index 0000000..feafa5f
--- /dev/null
+++ b/.devcontainer/vscode-init/extensions-to-install.txt
@@ -0,0 +1,15 @@
+# VS Code Extensions List
+# These extensions will be enabled for all users of the devcontainer.
+# One extension ID per line.
+charliermarsh.ruff
+Continue.continue
+DavidAnson.vscode-markdownlint
+eamodio.gitlens
+marimo-team.vscode-marimo
+mechatroner.rainbow-csv
+ms-python.black-formatter
+ms-toolsai.datawrangler
+ms-toolsai.jupyter
+REditorSupport.r
+REditorSupport.r-syntax
+yzhang.markdown-all-in-one
\ No newline at end of file
diff --git a/.devcontainer/vscode-init/vscode-extensions.txt b/.devcontainer/vscode-init/vscode-extensions.txt
deleted file mode 100644
index 793d1da..0000000
--- a/.devcontainer/vscode-init/vscode-extensions.txt
+++ /dev/null
@@ -1,9 +0,0 @@
-# VS Code Extensions List
-# One extension ID per line
-Continue.continue
-ms-python.black-formatter
-ms-toolsai.jupyter
-yzhang.markdown-all-in-one
-mechatroner.rainbow-csv
-marimo-team.vscode-marimo
-ms-toolsai.datawrangler
diff --git a/DEVCONTAINER.md b/DEVCONTAINER.md
index f409a34..8c2ad03 100644
--- a/DEVCONTAINER.md
+++ b/DEVCONTAINER.md
@@ -95,15 +95,18 @@ The container is automatically built and published using GitHub Actions:
 │   ├── Dockerfile                 # Custom Docker build
 │   └── vscode-init/               # VS Code server and extensions setup
 │       ├── 00-install-vscode-server.sh
-│       ├── 01-install-vscode-extensions.sh
-|       ├── 02-download-container-tools-extension.sh
-│       └── vscode-extensions.txt
+│       ├── 01-install-extensions.sh
+│       ├── 02-download-extensions.sh
+│       ├── extensions-to-download.txt
+│       └── extensions-to-install.txt
 ├── .github/workflows/
-│   └── build-devcontainer.yml     # Build and publish workflow
-├── examples/
-│   └── USAGE.md                   # Usage examples
-├── DEVCONTAINER.md                 # Detailed documentation
-└── README.md                      # Overview and quick start
+│   ├── build-devcontainer.yml     # Build and publish workflow
+│   └── build-publish-container.yml
+├── assets/                        # Documentation assets
+├── docs/                          # Additional documentation
+├── DEVCONTAINER.md                # Detailed documentation
+├── README.md                      # Overview and quick start
+└── SDF_TRE_SETUP.md              # SDF TRE setup guide
 ```
 
 ## 🔧 Customization