From f5b153099049c4f9a925f59f58fc152bb60e6aae Mon Sep 17 00:00:00 2001
From: aidenvaines-bjss <aiden.vaines@bjss.com>
Date: Wed, 23 Jul 2025 16:20:59 +0100
Subject: [PATCH 1/4] CCM-11345 Manual Repo Sync

---
 .github/actions/check-todo-usage/action.yaml  |  10 +
 .../create-lines-of-code-report/action.yaml   |   2 +-
 .github/actions/scan-dependencies/action.yaml |   2 +-
 .github/workflows/cicd-3-deploy.yaml          |   1 -
 .../scheduled-repository-template-sync.yaml   |   2 +-
 .github/workflows/scorecard.yml               |  14 +-
 .github/workflows/stage-1-commit.yaml         |  25 +-
 .github/workflows/stage-3-build.yaml          |   4 +-
 .gitignore                                    |  12 +-
 .tool-versions                                |  14 +-
 infrastructure/terraform/.gitignore           |   1 -
 infrastructure/terraform/bin/terraform.sh     |  42 ++--
 .../config/.repository-template-sync-ignore   |  21 +-
 .../config/.repository-template-sync-merge    |   9 +
 scripts/config/gitleaks.toml                  |   1 +
 scripts/config/pre-commit.yaml                |   8 +-
 scripts/config/terraform-docs.yml             |   2 +
 .../config/vocabularies/words/accept.txt      |   2 +-
 scripts/githooks/check-todos.sh               | 238 ++++++++++++++++++
 scripts/githooks/sort-dictionary.sh           |   3 +-
 scripts/githooks/sync-template-repo.sh        |  76 ++++--
 scripts/init.mk                               |   4 +-
 scripts/maintenance/merge.js                  |  81 ++++++
 scripts/terraform/terraform-docs.sh           |   2 +-
 24 files changed, 498 insertions(+), 78 deletions(-)
 create mode 100644 .github/actions/check-todo-usage/action.yaml
 create mode 100644 scripts/config/.repository-template-sync-merge
 create mode 100755 scripts/githooks/check-todos.sh
 create mode 100644 scripts/maintenance/merge.js

diff --git a/.github/actions/check-todo-usage/action.yaml b/.github/actions/check-todo-usage/action.yaml
new file mode 100644
index 00000000..a403d588
--- /dev/null
+++ b/.github/actions/check-todo-usage/action.yaml
@@ -0,0 +1,10 @@
+name: "Check Todo usage"
+description: "Check Todo usage"
+runs:
+  using: "composite"
+  steps:
+    - name: "Check Todo usage"
+      shell: bash
+      run: |
+        export BRANCH_NAME=origin/${{ github.event.repository.default_branch }}
+        check=branch ./scripts/githooks/check-todos.sh
diff --git a/.github/actions/create-lines-of-code-report/action.yaml b/.github/actions/create-lines-of-code-report/action.yaml
index b21f0667..86396f7a 100644
--- a/.github/actions/create-lines-of-code-report/action.yaml
+++ b/.github/actions/create-lines-of-code-report/action.yaml
@@ -44,7 +44,7 @@ runs:
         echo "secrets_exist=${{ inputs.idp_aws_report_upload_role_name != '' && inputs.idp_aws_report_upload_bucket_endpoint != '' }}" >> $GITHUB_OUTPUT
     - name: "Authenticate to send the report"
       if: steps.check.outputs.secrets_exist == 'true'
-      uses: aws-actions/configure-aws-credentials@v2
+      uses: aws-actions/configure-aws-credentials@v4
       with:
         role-to-assume: arn:aws:iam::${{ inputs.idp_aws_report_upload_account_id }}:role/${{ inputs.idp_aws_report_upload_role_name }}
         aws-region: ${{ inputs.idp_aws_report_upload_region }}
diff --git a/.github/actions/scan-dependencies/action.yaml b/.github/actions/scan-dependencies/action.yaml
index f8ed605d..1000df14 100644
--- a/.github/actions/scan-dependencies/action.yaml
+++ b/.github/actions/scan-dependencies/action.yaml
@@ -58,7 +58,7 @@ runs:
       run: echo "secrets_exist=${{ inputs.idp_aws_report_upload_role_name != '' && inputs.idp_aws_report_upload_bucket_endpoint != '' }}" >> $GITHUB_OUTPUT
     - name: "Authenticate to send the reports"
       if: steps.check.outputs.secrets_exist == 'true'
-      uses: aws-actions/configure-aws-credentials@v2
+      uses: aws-actions/configure-aws-credentials@v4
       with:
         role-to-assume: arn:aws:iam::${{ inputs.idp_aws_report_upload_account_id }}:role/${{ inputs.idp_aws_report_upload_role_name }}
         aws-region: ${{ inputs.idp_aws_report_upload_region }}
diff --git a/.github/workflows/cicd-3-deploy.yaml b/.github/workflows/cicd-3-deploy.yaml
index ff2ad644..5230577e 100644
--- a/.github/workflows/cicd-3-deploy.yaml
+++ b/.github/workflows/cicd-3-deploy.yaml
@@ -48,7 +48,6 @@ jobs:
           echo "nodejs_version=$(grep "^nodejs\s" .tool-versions | cut -f2 -d' ')" >> $GITHUB_OUTPUT
           echo "python_version=$(grep "^python\s" .tool-versions | cut -f2 -d' ')" >> $GITHUB_OUTPUT
           echo "terraform_version=$(grep "^terraform\s" .tool-versions | cut -f2 -d' ')" >> $GITHUB_OUTPUT
-          # TODO: Get the version, but it may not be the .version file as this should come from the CI/CD Pull Request Workflow
           echo "version=$(head -n 1 .version 2> /dev/null || echo unknown)" >> $GITHUB_OUTPUT
           # echo "tag=${{ github.event.inputs.tag }}" >> $GITHUB_OUTPUT
       - name: "List variables"
diff --git a/.github/workflows/scheduled-repository-template-sync.yaml b/.github/workflows/scheduled-repository-template-sync.yaml
index 9df295a9..e9114865 100644
--- a/.github/workflows/scheduled-repository-template-sync.yaml
+++ b/.github/workflows/scheduled-repository-template-sync.yaml
@@ -27,7 +27,7 @@ jobs:
 
     - name: Run syncronisation script
       run: |
-        ./scripts/githooks/sync-template-repo.sh
+        ./nhs-notify-repository-template/scripts/githooks/sync-template-repo.sh
         rm -Rf ./nhs-notify-repository-template
 
     - name: Create Pull Request
diff --git a/.github/workflows/scorecard.yml b/.github/workflows/scorecard.yml
index 9c6fdd97..03bf1714 100644
--- a/.github/workflows/scorecard.yml
+++ b/.github/workflows/scorecard.yml
@@ -27,17 +27,17 @@ jobs:
       # Needed to publish results and get a badge (see publish_results below).
       id-token: write
       # Uncomment the permissions below if installing in a private repository.
-      # contents: read
-      # actions: read
+      contents: read
+      actions: read
 
     steps:
       - name: "Checkout code"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
         with:
           persist-credentials: false
 
       - name: "Run analysis"
-        uses: ossf/scorecard-action@f49aabe0b5af0936a0987cfb85d86b75731b0186 # v2.4.1
+        uses: ossf/scorecard-action@62b2cac7ed8198b15735ed49ab1e5cf35480ba46 # v2.4.0
         with:
           results_file: results.sarif
           results_format: sarif
@@ -45,7 +45,7 @@ jobs:
           # - you want to enable the Branch-Protection check on a *public* repository, or
           # - you are installing Scorecard on a *private* repository
           # To create the PAT, follow the steps in https://github.com/ossf/scorecard-action?tab=readme-ov-file#authentication-with-fine-grained-pat-optional.
-          # repo_token: ${{ secrets.SCORECARD_TOKEN }}
+          repo_token: ${{ secrets.SCORECARD_TOKEN }}
 
           # Public repositories:
           #   - Publish results to OpenSSF REST API for easy access by consumers
@@ -59,7 +59,7 @@ jobs:
       # Upload the results as artifacts (optional). Commenting out will disable uploads of run results in SARIF
       # format to the repository Actions tab.
       - name: "Upload artifact"
-        uses: actions/upload-artifact@97a0fba1372883ab732affbe8f94b823f91727db # v3.pre.node20
+        uses: actions/upload-artifact@v4
         with:
           name: SARIF file
           path: results.sarif
@@ -68,6 +68,6 @@ jobs:
       # Upload the results to GitHub's code scanning dashboard (optional).
       # Commenting out will disable upload of results to your repo's Code Scanning dashboard
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@60168efe1c415ce0f5521ea06d5c2062adbeed1b # v3.28.17
+        uses: github/codeql-action/upload-sarif@9e8d0789d4a0fa9ceb6b1738f7e269594bdd67f0 # v3.28.9
         with:
           sarif_file: results.sarif
diff --git a/.github/workflows/stage-1-commit.yaml b/.github/workflows/stage-1-commit.yaml
index e168ba96..e56f2f3e 100644
--- a/.github/workflows/stage-1-commit.yaml
+++ b/.github/workflows/stage-1-commit.yaml
@@ -36,7 +36,7 @@ jobs:
   scan-secrets:
     name: "Scan secrets"
     runs-on: ubuntu-latest
-    timeout-minutes: 2
+    timeout-minutes: 5
     steps:
       - name: "Checkout code"
         uses: actions/checkout@v4
@@ -47,7 +47,7 @@ jobs:
   check-file-format:
     name: "Check file format"
     runs-on: ubuntu-latest
-    timeout-minutes: 2
+    timeout-minutes: 5
     steps:
       - name: "Checkout code"
         uses: actions/checkout@v4
@@ -58,7 +58,7 @@ jobs:
   check-markdown-format:
     name: "Check Markdown format"
     runs-on: ubuntu-latest
-    timeout-minutes: 2
+    timeout-minutes: 5
     steps:
       - name: "Checkout code"
         uses: actions/checkout@v4
@@ -93,7 +93,7 @@ jobs:
   check-english-usage:
     name: "Check English usage"
     runs-on: ubuntu-latest
-    timeout-minutes: 2
+    timeout-minutes: 5
     steps:
       - name: "Checkout code"
         uses: actions/checkout@v4
@@ -101,6 +101,17 @@ jobs:
           fetch-depth: 0 # Full history is needed to compare branches
       - name: "Check English usage"
         uses: ./.github/actions/check-english-usage
+  check-todo-usage:
+    name: "Check TODO usage"
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+    steps:
+      - name: "Checkout code"
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # Full history is needed to compare branches
+      - name: "Check TODO usage"
+        uses: ./.github/actions/check-todo-usage
   detect-terraform-changes:
     name: "Detect Terraform Changes"
     runs-on: ubuntu-latest
@@ -127,7 +138,7 @@ jobs:
   lint-terraform:
     name: "Lint Terraform"
     runs-on: ubuntu-latest
-    timeout-minutes: 2
+    timeout-minutes: 5
     needs: detect-terraform-changes
     if: needs.detect-terraform-changes.outputs.terraform_changed == 'true'
     steps:
@@ -156,7 +167,7 @@ jobs:
     permissions:
       id-token: write
       contents: read
-    timeout-minutes: 2
+    timeout-minutes: 5
     steps:
       - name: "Checkout code"
         uses: actions/checkout@v4
@@ -175,7 +186,7 @@ jobs:
     permissions:
       id-token: write
       contents: read
-    timeout-minutes: 2
+    timeout-minutes: 5
     steps:
       - name: "Checkout code"
         uses: actions/checkout@v4
diff --git a/.github/workflows/stage-3-build.yaml b/.github/workflows/stage-3-build.yaml
index 201d5b19..fabfe110 100644
--- a/.github/workflows/stage-3-build.yaml
+++ b/.github/workflows/stage-3-build.yaml
@@ -60,7 +60,7 @@ jobs:
       - name: "Upload artefact 1"
         run: |
           echo "Uploading artefact 1 ..."
-          # TODO: Use either action/cache or action/upload-artifact
+          # Use either action/cache or action/upload-artifact
   artefact-n:
     name: "Artefact n"
     runs-on: ubuntu-latest
@@ -77,4 +77,4 @@ jobs:
       - name: "Upload artefact n"
         run: |
           echo "Uploading artefact n ..."
-          # TODO: Use either action/cache or action/upload-artifact
+          # Use either action/cache or action/upload-artifact
diff --git a/.gitignore b/.gitignore
index adb1a949..e97bd341 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,6 +9,16 @@
 version.json
 *.code-workspace
 !project.code-workspace
-node_modules
 
 # Please, add your custom content below!
+
+# dependencies
+node_modules
+.node-version
+*/node_modules
+/.pnp
+.pnp.js
+/build
+dist
+.DS_Store
+.reports
diff --git a/.tool-versions b/.tool-versions
index 6b801709..34d9b8a5 100644
--- a/.tool-versions
+++ b/.tool-versions
@@ -1,19 +1,21 @@
 act 0.2.64
-gitleaks 8.18.4
+gitleaks 8.24.0
+jq 1.6
+nodejs 22.11.0
 pre-commit 3.6.0
 terraform 1.9.2
 terraform-docs 0.19.0
 trivy 0.61.0
 vale 3.6.0
-nodejs 22.15.1
+# python 3.13.2
 
 # ==============================================================================
 # The section below is reserved for Docker image versions.
 
 # TODO: Move this section - consider using a different file for the repository template dependencies.
-# docker/ghcr.io/anchore/grype v0.69.1@sha256:d41fcb371d0af59f311e72123dff46900ebd6d0482391b5a830853ee4f9d1a76 # SEE: https://github.com/anchore/grype/pkgs/container/grype
-# docker/ghcr.io/anchore/syft v0.92.0@sha256:63c60f0a21efb13e80aa1359ab243e49213b6cc2d7e0f8179da38e6913b997e0 # SEE: https://github.com/anchore/syft/pkgs/container/syft
-# docker/ghcr.io/gitleaks/gitleaks v8.18.0@sha256:fd2b5cab12b563d2cc538b14631764a1c25577780e3b7dba71657d58da45d9d9 # SEE: https://github.com/gitleaks/gitleaks/pkgs/container/gitleaks
+# docker/ghcr.io/anchore/grype v0.92.2@sha256:651e558f9ba84f2a790b3449c8a57cbbf4f34e004f7d3f14ae8f8cbeede4cd33  # SEE: https://github.com/anchore/grype/pkgs/container/grype
+# docker/ghcr.io/anchore/syft v1.26.0@sha256:de078f51704a213906970b1475edd6006b8af50aa159852e125518237487b8c6  # SEE: https://github.com/anchore/syft/pkgs/container/syft
+# docker/ghcr.io/gitleaks/gitleaks:v8.24.0@sha256:b8e9bf46893c2f20e10bfb4b2e783adaef519dea981b01ca6221ac325e836040 # SEE: https://github.com/gitleaks/gitleaks/pkgs/container/gitleaks
 # docker/ghcr.io/igorshubovych/markdownlint-cli v0.37.0@sha256:fb3e79946fce78e1cde84d6798c6c2a55f2de11fc16606a40d49411e281d950d # SEE: https://github.com/igorshubovych/markdownlint-cli/pkgs/container/markdownlint-cli
 # docker/ghcr.io/make-ops-tools/gocloc latest@sha256:6888e62e9ae693c4ebcfed9f1d86c70fd083868acb8815fe44b561b9a73b5032 # SEE: https://github.com/make-ops-tools/gocloc/pkgs/container/gocloc
 # docker/ghcr.io/nhs-england-tools/github-runner-image 20230909-321fd1e-rt@sha256:ce4fd6035dc450a50d3cbafb4986d60e77cb49a71ab60a053bb1b9518139a646 # SEE: https://github.com/nhs-england-tools/github-runner-image/pkgs/container/github-runner-image
@@ -22,4 +24,4 @@ nodejs 22.15.1
 # docker/jdkato/vale v3.6.0@sha256:0ef22c8d537f079633cfff69fc46f69a2196072f69cab1ab232e8a79a388e425 # SEE: https://hub.docker.com/r/jdkato/vale/tags
 # docker/koalaman/shellcheck latest@sha256:e40388688bae0fcffdddb7e4dea49b900c18933b452add0930654b2dea3e7d5c # SEE: https://hub.docker.com/r/koalaman/shellcheck/tags
 # docker/mstruebing/editorconfig-checker 2.7.1@sha256:dd3ca9ea50ef4518efe9be018d669ef9cf937f6bb5cfe2ef84ff2a620b5ddc24 # SEE: https://hub.docker.com/r/mstruebing/editorconfig-checker/tags
-# docker/sonarsource/sonar-scanner-cli 5.0.1@sha256:494ecc3b5b1ee1625bd377b3905c4284e4f0cc155cff397805a244dee1c7d575 # SEE: https://hub.docker.com/r/sonarsource/sonar-scanner-cli/tags
+# docker/sonarsource/sonar-scanner-cli 11.3@sha256:7462f132388135e32b948f8f18ff0db9ae28a87c6777f1df5b2207e04a6d7c5c # SEE: https://hub.docker.com/r/sonarsource/sonar-scanner-cli/tags
diff --git a/infrastructure/terraform/.gitignore b/infrastructure/terraform/.gitignore
index 54175d30..579b6414 100644
--- a/infrastructure/terraform/.gitignore
+++ b/infrastructure/terraform/.gitignore
@@ -23,7 +23,6 @@ components/**/backend_tfscaffold.tf
 
 # Scaffold Plugin Cache
 plugin-cache/*
-bootstrap
 
 # PyCache
 **/__pycache__
diff --git a/infrastructure/terraform/bin/terraform.sh b/infrastructure/terraform/bin/terraform.sh
index c932a77e..72e6c571 100755
--- a/infrastructure/terraform/bin/terraform.sh
+++ b/infrastructure/terraform/bin/terraform.sh
@@ -539,24 +539,26 @@ fi;
 [ -f "${dynamic_file_path}" ] && tf_var_file_paths+=("${dynamic_file_path}");
 
 # Warn on duplication
-duplicate_variables="$(cat "${tf_var_file_paths[@]}" | sed -n -e 's/\(^[a-zA-Z0-9_\-]\+\)\s*=.*$/\1/p' | sort | uniq -d)";
-[ -n "${duplicate_variables}" ] \
-  && echo -e "
-###################################################################
-# WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING #
-###################################################################
-The following input variables appear to be duplicated:
-
-${duplicate_variables}
-
-This could lead to unexpected behaviour. Overriding of variables
-has previously been unpredictable and is not currently supported,
-but it may work.
-
-Recent changes to terraform might give you useful overriding and
-map-merging functionality, please use with caution and report back
-on your successes & failures.
-###################################################################";
+if [ ${#tf_var_file_paths[@]} -gt 0 ]; then
+  duplicate_variables="$(cat "${tf_var_file_paths[@]}" | sed -n -e 's/\(^[a-zA-Z0-9_\-]\+\)\s*=.*$/\1/p' | sort | uniq -d)";
+  [ -n "${duplicate_variables}" ] \
+    && echo -e "
+  ###################################################################
+  # WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING #
+  ###################################################################
+  The following input variables appear to be duplicated:
+
+  ${duplicate_variables}
+
+  This could lead to unexpected behaviour. Overriding of variables
+  has previously been unpredictable and is not currently supported,
+  but it may work.
+
+  Recent changes to terraform might give you useful overriding and
+  map-merging functionality, please use with caution and report back
+  on your successes & failures.
+  ###################################################################";
+fi
 
 # Build up the tfvars arguments for terraform command line
 for file_path in "${tf_var_file_paths[@]}"; do
@@ -791,8 +793,8 @@ case "${action}" in
     ;;
   *)
     echo -e "Generic action case invoked. Only the additional arguments will be passed to terraform, you break it you fix it:";
-    echo -e "\tterraform ${action} ${extra_args}";
-    terraform "${action}" ${extra_args} \
+    echo -e "\tterraform ${action} ${extra_args} | tee terraform_output";
+    terraform "${action}" ${extra_args} | tee terraform_output \
       || error_and_die "Terraform ${action} failed.";
     ;;
 esac;
diff --git a/scripts/config/.repository-template-sync-ignore b/scripts/config/.repository-template-sync-ignore
index 7564f3e8..7b6cbfc1 100644
--- a/scripts/config/.repository-template-sync-ignore
+++ b/scripts/config/.repository-template-sync-ignore
@@ -1,18 +1,33 @@
 # Files and folders to ignore when syncing nhs-notify-repository-template back in to this repository
-scripts/config/.repository-template-sync-ignore
-.github/workflows/
 nhs-notify-repository-template/
 
 # Files and Folders in this repository to ignore
+.editorconfig
+.github/CODEOWNERS
+.github/ISSUE_TEMPLATE
+.github/workflows/cicd-*.yaml
+.github/workflows/stage-*.yaml
+.gitleaksignore
 .vscode/
+Makefile
 CHANGELOG.md
 project.code-workspace
 README.md
+scripts/config/sonar-scanner.properties
+scripts/tests/
 VERSION
 
 # Files and Folders in the template repository to disregard
 .devcontainer/
-.github/workflows/cicd-*.yaml
+.github/actions/build-docs
+.github/workflows/*.disabled
 */examples/
 docs/
+eslint.config.mjs
 infrastructure/terraform/components/
+lambdas/example-lambda/
+package-lock.json
+package.json
+scripts/**/examples/
+scripts/terraform/terraform.mk
+src/.vscode/
diff --git a/scripts/config/.repository-template-sync-merge b/scripts/config/.repository-template-sync-merge
new file mode 100644
index 00000000..a42f50a9
--- /dev/null
+++ b/scripts/config/.repository-template-sync-merge
@@ -0,0 +1,9 @@
+# Files and folders to merge when syncing nhs-notify-repository-template back in to this repository
+.github/workflows/cicd-*.yaml
+.gitignore
+.tool-versions
+scripts/config/.repository-template-sync-ignore
+scripts/config/.repository-template-sync-merge
+scripts/config/vale/styles/config/vocabularies/words/accept.txt
+scripts/config/vale/styles/config/vocabularies/words/reject.txt
+scripts/config/vale/vale.ini
diff --git a/scripts/config/gitleaks.toml b/scripts/config/gitleaks.toml
index 188bfdf0..7b8360ae 100644
--- a/scripts/config/gitleaks.toml
+++ b/scripts/config/gitleaks.toml
@@ -1,4 +1,5 @@
 # SEE: https://github.com/gitleaks/gitleaks/#configuration
+# Do not edit this file directly as it will be overwritten by changes from the nhs-notify-repository-template on next sync
 
 [extend]
 useDefault = true # SEE: https://github.com/gitleaks/gitleaks/blob/master/config/gitleaks.toml
diff --git a/scripts/config/pre-commit.yaml b/scripts/config/pre-commit.yaml
index de68260b..8843370f 100644
--- a/scripts/config/pre-commit.yaml
+++ b/scripts/config/pre-commit.yaml
@@ -9,7 +9,6 @@ repos:
       - id: check-symlinks
       - id: detect-private-key
       - id: end-of-file-fixer
-        exclude: .+\.cs
       - id: forbid-new-submodules
       - id: mixed-line-ending
       - id: pretty-format-json
@@ -64,3 +63,10 @@ repos:
         entry: ./scripts/githooks/check-terraform-docs.sh
         language: script
         pass_filenames: false
+  - repo: local
+    hooks:
+      - id: check-todo-usage
+        name: Check TODO usage
+        entry: /usr/bin/env check=branch ./scripts/githooks/check-todos.sh
+        language: script
+        pass_filenames: false
diff --git a/scripts/config/terraform-docs.yml b/scripts/config/terraform-docs.yml
index b38d1289..e49d91f8 100644
--- a/scripts/config/terraform-docs.yml
+++ b/scripts/config/terraform-docs.yml
@@ -16,6 +16,7 @@ content: |-
   {{ .Modules }}
   {{ .Outputs }}
   {{ .Footer }}
+
 output:
   file: 'README.md'
   mode: inject
@@ -27,6 +28,7 @@ output:
     <!-- vale on -->
     <!-- markdownlint-enable -->
     <!-- END_TF_DOCS -->
+
 output-values:
   enabled: false
   from: ''
diff --git a/scripts/config/vale/styles/config/vocabularies/words/accept.txt b/scripts/config/vale/styles/config/vocabularies/words/accept.txt
index 3b07d50c..3aa82c3a 100644
--- a/scripts/config/vale/styles/config/vocabularies/words/accept.txt
+++ b/scripts/config/vale/styles/config/vocabularies/words/accept.txt
@@ -9,7 +9,7 @@ drawio
 endcapture
 endfor
 endraw
-GitHub
+Git[Hh]ub
 Gitleaks
 Grype
 idempotence
diff --git a/scripts/githooks/check-todos.sh b/scripts/githooks/check-todos.sh
new file mode 100755
index 00000000..83b7a80e
--- /dev/null
+++ b/scripts/githooks/check-todos.sh
@@ -0,0 +1,238 @@
+#!/bin/bash
+
+# WARNING: Please, DO NOT edit this file! It is maintained in the Repository Template (https://github.com/nhs-england-tools/repository-template). Raise a PR instead.
+
+set -euo pipefail
+
+# Pre-commit git hook to scan for secrets hard-coded in the codebase. This is a
+# gitleaks command wrapper. It will run gitleaks natively if it is installed,
+# otherwise it will run it in a Docker container.
+#
+# Usage:
+#   $ [options] ./scan-secrets.sh
+#
+# Options:
+#   check=all                   # check all files in the repository
+#   check=staged-changes        # check only files staged for commit.
+#   check=working-tree-changes  # check modified, unstaged files. This is the default.
+#   check=branch                # check for all changes since branching from $BRANCH_NAME
+#   VERBOSE=true                # Show all the executed commands, default is 'false'
+#
+# Exit codes:
+#   0 - No Todos
+#   1 - Todos found or error encountered
+#   126 - Unknown flag
+
+# ==============================================================================
+
+EXCLUDED_FILES=(
+  ".devcontainer/devcontainer.json"
+  ".tool-versions"
+  ".vscode/extensions.json"
+  "infrastructure/terraform/bin/terraform.sh"
+  "Makefile"
+  "project.code-workspace"
+  "src/jekyll-devcontainer/src/.devcontainer/devcontainer.json"
+)
+
+EXCLUDED_DIRS=(
+  ".git/"
+  ".venv/"
+  "docs/"
+  "node_modules/"
+)
+
+
+# Get files to check based on mode
+function get_files_to_check() {
+  local mode="$1"
+  case "$mode" in
+    staged-changes)
+      git diff --diff-filter=ACMRT --name-only --cached # ACMRT only show files added, copied, modified, renamed or that had their type changed (eg. file → symlink) in this commit. This leaves out deleted files.
+      ;;
+    working-tree-changes)
+      git ls-files --others --exclude-standard && git diff --diff-filter=ACMRT --name-only
+      ;;
+    branch)
+      git diff --diff-filter=ACMRT --name-only ${BRANCH_NAME:-origin/main}
+      ;;
+    all)
+      git ls-files && git ls-files --others --exclude-standard
+      ;;
+    *)
+      echo "Unknown check mode: $mode" >&2
+      exit 126
+      ;;
+  esac
+}
+
+
+function build_exclude_args() {
+  local args=(
+    --exclude=".github/actions/check-todo-usage/action.yaml"
+    --exclude=".github/workflows/stage-1-commit.yaml"
+    --exclude="scripts/config/pre-commit.yaml"
+    --exclude="scripts/githooks/check-todos.sh"
+  ) # Exclude this script and its references by default, as it naturally contains TODOs. Todo todo todo <- see?
+
+  if [ ${#EXCLUDED_DIRS[@]} -gt 0 ]; then
+    for dir in "${EXCLUDED_DIRS[@]}"; do
+      args+=(--exclude-dir="$dir")
+    done
+  fi
+
+  if [ ${#EXCLUDED_FILES[@]} -gt 0 ]; then
+    for file in "${EXCLUDED_FILES[@]}"; do
+      args+=(--exclude="$file")
+    done
+  fi
+  echo "${args[@]}"
+}
+
+
+function search_todos() {
+  local mode="$1"
+  shift # Shift positional parameters so $@ contains only exclude_args
+  local exclude_args=("$@")
+  local todos=""
+
+  local files
+  files=$(get_files_to_check "$mode")
+  # flatten files to unique list
+  files=$(echo "$files" | tr ' ' '\n' | sort -u)
+
+  for file in $files; do
+    skip=false
+
+    # Check if the file matches any exclude patterns
+    # Exclude files based on provided arguments and predefined directories
+    for ex in "${exclude_args[@]}"; do
+      if [[ "$ex" == --exclude* ]]; then
+        pattern=${ex#--exclude=}
+        [[ "$file" == $pattern ]] && skip=true && break
+      fi
+    done
+
+    # Check if the file is in any of the excluded directories
+    for exdir in "${EXCLUDED_DIRS[@]}"; do
+      [[ "$file" == $exdir* ]] && skip=true && break
+    done
+
+    # If the file is excluded, skip it
+    if [ "$skip" = false ] && [ -f "$file" ]; then
+      file_todos=$(grep -nHiE '\bTODO\b' "$file" || true)
+      [ -n "$file_todos" ] && todos+="$file_todos\n"
+    fi
+  done
+
+  echo -e "$todos"
+}
+
+
+function filter_todos_with_valid_jira_ticket() {
+  local todos="$1"
+  local jira_regex="[A-Z][A-Z0-9]+-[0-9]+"
+  local todos_without_ticket=""
+
+  while IFS= read -r line; do
+    # Only lines with TODO but without a valid JIRA ticket
+    if grep -qnHiE '\bTODO\b' <<< "$line"; then
+      if ! [[ "$line" =~ $jira_regex ]]; then
+        todos_without_ticket+="$line\n"
+      fi
+    fi
+  done <<< "$(echo -e "$todos")"
+
+  # Output only TODOs without a valid JIRA ticket
+  echo -e "$todos_without_ticket"
+}
+
+
+function print_output() {
+  local todos="$1"
+  local exclude_args="$2"
+  local todo_count=$(line_count "$todos")
+
+  echo "TODO Check Configuration:"
+  echo "========================================="
+  echo "  Check Mode: ${check:-working-tree-changes}"
+  echo "  Total TODOs found: $todo_count"
+
+  if [ ${#EXCLUDED_DIRS[@]} -gt 0 ]; then
+    echo "  Excluded Directories: ${EXCLUDED_DIRS[*]}"
+  else
+    echo "  Excluded Directories: (none)"
+  fi
+
+  if [ ${#EXCLUDED_FILES[@]} -gt 0 ]; then
+    echo "  Excluded Files: ${EXCLUDED_FILES[*]}"
+  else
+    echo "  Excluded Files: (none)"
+  fi
+
+  if is-arg-true "${VERBOSE:-false}"; then
+    echo "Grep Exclude Args: $exclude_args"
+  fi
+
+  echo -e "\n========================================="
+  echo "All TODOs found: $todo_count"
+  echo "========================================="
+
+  if [ "$todo_count" -gt 0 ]; then
+    echo "$todos"
+  else
+    echo "No TODOs found."
+  fi
+
+  local results=$(filter_todos_with_valid_jira_ticket "$todos")
+  local results_count=$(line_count "$results")
+
+  echo -e "\n========================================="
+  echo "TODOs without a Jira ticket: $results_count"
+  echo "========================================="
+
+  if [ "$results_count" -gt 0 ]; then
+    echo "$results"
+    exit 1
+  else
+      echo "No TODOs found without a Jira reference."
+  fi
+}
+
+
+function main() {
+  cd "$(git rev-parse --show-toplevel)"
+
+  local check_mode="${check:-working-tree-changes}"
+  local exclude_args=$(build_exclude_args)
+  local todos=$(search_todos "$check_mode" $exclude_args)
+  print_output "$todos" "$exclude_args"
+}
+
+# ==============================================================================
+
+# Count non-empty lines in a string
+function line_count() {
+  local input="$1"
+  if [ -n "$input" ]; then
+    echo -e "$input" | wc -l
+  else
+    echo 0
+  fi
+}
+
+function is-arg-true() {
+  if [[ "$1" =~ ^(true|yes|y|on|1|TRUE|YES|Y|ON)$ ]]; then
+    return 0
+  else
+    return 1
+  fi
+}
+
+# ==============================================================================
+
+is-arg-true "${VERBOSE:-false}" && set -x
+
+main "$@"
+
+exit 0
diff --git a/scripts/githooks/sort-dictionary.sh b/scripts/githooks/sort-dictionary.sh
index 45a39529..2fea1399 100755
--- a/scripts/githooks/sort-dictionary.sh
+++ b/scripts/githooks/sort-dictionary.sh
@@ -25,7 +25,8 @@ function main() {
   mv $root/accept.sorted.txt $root/accept.txt
   mv $root/reject.sorted.txt $root/reject.txt
 
-  git add -uv $root/*
+  # Update the sorted files in the staged git index
+  git add --update --verbose $root/*
 }
 
 # ==============================================================================
diff --git a/scripts/githooks/sync-template-repo.sh b/scripts/githooks/sync-template-repo.sh
index 060aaa4c..6e731db7 100755
--- a/scripts/githooks/sync-template-repo.sh
+++ b/scripts/githooks/sync-template-repo.sh
@@ -5,7 +5,7 @@ set -euo pipefail
 # Script to synchronise the nhs-notify-template-repository with this repository
 #
 # Usage:
-#   $ [options] ./check-terraform-format.sh
+#   $ [options] ./sync-template-repo.sh
 #
 # Options:
 #   new_only=true      # Only identify new files from the template-repository
@@ -13,13 +13,16 @@ set -euo pipefail
 
 # ==============================================================================
 
-# Command line prameters
+scriptdir=$(realpath "$(dirname "$0")")
+
+# Command line parameters
 new_only=${new_only:-false}
 changes_only=${changes_only:-false}
 
 # Set variables
 TEMPLATE_REPO_DIR="nhs-notify-repository-template"
 IGNORE_FILE="scripts/config/.repository-template-sync-ignore"
+MERGE_FILE="scripts/config/.repository-template-sync-merge"
 
 # Check if the template directory exists
 if [ ! -d "${TEMPLATE_REPO_DIR}" ]; then
@@ -34,10 +37,18 @@ if [ ! -f "${IGNORE_FILE}" ]; then
   echo "# Files and Folders in the template repository to disregard" >> ${IGNORE_FILE}
 fi
 
-# Read the .template-ignore file into an array
-while IFS= read -r line || [ -n "$line" ]; do
-  IGNORED_PATHS+=("$line")
-done < "$IGNORE_FILE"
+# Check if the .template-merge file exists, create an empty one if not
+if [ ! -f "${MERGE_FILE}" ]; then
+  echo "# Files and folders to merge when syncing ${TEMPLATE_REPO_DIR} back in to this repository" > ${MERGE_FILE}
+fi
+
+TMP_SYNC_IGNORE=${PWD}/tmp-sync-ignore
+mkdir -p "${TMP_SYNC_IGNORE}"
+cp "${IGNORE_FILE}" "${TMP_SYNC_IGNORE}/.gitignore"
+
+TMP_SYNC_MERGE=${PWD}/tmp-sync-merge
+mkdir -p "${TMP_SYNC_MERGE}"
+cp "${MERGE_FILE}" "${TMP_SYNC_MERGE}/.gitignore"
 
 # Check if a file is ignored.
 is_ignored() {
@@ -48,21 +59,30 @@ is_ignored() {
     return 0
   fi
 
-  for ignored in "${IGNORED_PATHS[@]}"; do
-    if [[ -n "$ignored" && "$file" =~ $ignored ]]; then
-      return 0
-    fi
-  done
-  return 1
+  pushd "${TMP_SYNC_IGNORE}" > /dev/null
+  git check-ignore -q "${file}"
+  R=$?
+  popd > /dev/null
+  return $R
+}
+
+is_merge() {
+  local file=${1}
+
+  pushd "${TMP_SYNC_MERGE}" > /dev/null
+  git check-ignore -q "${file}"
+  R=$?
+  popd > /dev/null
+  return $R
 }
 
 # Navigate to the template directory
-cd "${TEMPLATE_REPO_DIR}" || exit
+pushd "${TEMPLATE_REPO_DIR}" || exit
 FILES_ADDED=()
 FILES_WITH_CHANGES=()
 
 # Loop through all files in the template directory
-while IFS= read -r -d '' file; do
+while IFS= read -r -d '' file || [[ -n $file ]]; do
   relative_path="${file#./}"  # Remove leading './'
 
   # Check if the file is ignored
@@ -84,27 +104,41 @@ while IFS= read -r -d '' file; do
     # If the file exists, check if it's different
     if [ "$new_only" == false ]; then
       if ! diff -q "$file" "$target_path" > /dev/null 2>&1; then
-        echo "Merging changes from $relative_path"
-        FILES_WITH_CHANGES+=("${relative_path}")
-        cp "$file" "$target_path"
+        if is_merge "$relative_path"; then
+          echo "Merging changes from $relative_path"
+          cp "$target_path" "${target_path}.bak"
+          node "${scriptdir}/../maintenance/merge.js" "$target_path" "$file" > "${target_path}.merged"
+          if ! cmp -s "${target_path}.merged" "${target_path}.bak"; then
+            FILES_WITH_CHANGES+=("${relative_path}")
+            mv "${target_path}.merged" "$target_path"
+          fi
+          rm -f "${target_path}.merged" "${target_path}.bak"
+        else
+          echo "Copying changes from $relative_path"
+          cp "$file" "$target_path"
+          FILES_WITH_CHANGES+=("${relative_path}")
+        fi
       fi
     fi
   fi
 done < <(find . -type f -print0)
 
-echo "${#FILES_ADDED[@]}" files added, "${#FILES_WITH_CHANGES[@]}" files with changes detected.
+popd
+rm -rf "${TMP_SYNC_IGNORE}" "${TMP_SYNC_MERGE}"
 
 echo ------------------------------------------
+echo "${#FILES_ADDED[@]} files added, ${#FILES_WITH_CHANGES[@]} files with changes detected."
 
-if [ "$changes_only" == false ]; then
+if [[ "$changes_only" == false && ${#FILES_ADDED[@]} -gt 0 ]]; then
   echo ------------------------------------------
   echo "New files added:"
   printf ' - %s\n' "${FILES_ADDED[@]}"
 fi
 
-
-if [ "$new_only" == false ]; then
+if [[ "$new_only" == false && ${#FILES_WITH_CHANGES[@]} -gt 0 ]]; then
   echo ------------------------------------------
   echo "Changed files:"
   printf ' - %s\n' "${FILES_WITH_CHANGES[@]}"
 fi
+
+echo ------------------------------------------
diff --git a/scripts/init.mk b/scripts/init.mk
index 373f8a4f..e12255c3 100644
--- a/scripts/init.mk
+++ b/scripts/init.mk
@@ -7,7 +7,7 @@ include scripts/tests/test.mk
 # ==============================================================================
 
 runner-act: # Run GitHub Actions locally - mandatory: workflow=[workflow file name], job=[job name] @Development
-	source ./scripts/docker/docker.lib.sh
+	. ./scripts/docker/docker.lib.sh
 	act $(shell [[ "${VERBOSE}" =~ ^(true|yes|y|on|1|TRUE|YES|Y|ON)$$ ]] && echo --verbose) \
 		--container-architecture linux/amd64 \
 		--platform ubuntu-latest=$$(name="ghcr.io/nhs-england-tools/github-runner-image" docker-get-image-version-and-pull) \
@@ -21,7 +21,7 @@ runner-act: # Run GitHub Actions locally - mandatory: workflow=[workflow file na
 		--job ${job}
 
 version-create-effective-file: # Create effective version file - optional: dir=[path to the VERSION file to use, default is '.'], BUILD_DATETIME=[build date and time in the '%Y-%m-%dT%H:%M:%S%z' format generated by the CI/CD pipeline, default is current date and time] @Development
-	source scripts/docker/docker.lib.sh
+	. ./scripts/docker/docker.lib.sh
 	version-create-effective-file
 
 shellscript-lint-all: # Lint all shell scripts in this project, do not fail on error, just print the error messages @Quality
diff --git a/scripts/maintenance/merge.js b/scripts/maintenance/merge.js
new file mode 100644
index 00000000..8f5bd6cc
--- /dev/null
+++ b/scripts/maintenance/merge.js
@@ -0,0 +1,81 @@
+/*******************************************************************************
+ * Script to merge all added lines from source to target.
+ * Modified lines will be left intact.
+ *
+ * This is intended for updating config files like .tool-versions and .gitignore
+ * where the first token on the line remains the same
+ *
+ * Usage:
+ *   $ node merge.js <target> <source>
+ *
+ * Output:
+ *   Outputs the merged file to stdout
+ *
+ *******************************************************************************/
+
+const fs = require("fs");
+
+// Read files
+const [file1, file2] = process.argv.slice(2);
+const lines1 = fs.readFileSync(file1).toString().split('\n');
+const lines2 = fs.readFileSync(file2).toString().split('\n');
+
+// Tokenize lines in file1 for later comparison
+const tokenize = line => {
+  if (line === '') {
+    return [];
+  }
+  return line.split(/\s+|[:=]/).filter(x => x !== '#' && x !== '').slice(0, 1);
+};
+const lines1Tokens = lines1.flatMap(tokenize);
+
+// Step through the files
+let pos1 = 0, pos2 = 0;
+while (pos1 < lines1.length || pos2 < lines2.length) {
+
+  const l1 = pos1 < lines1.length && lines1[pos1] || '';
+  const l2 = pos2 < lines2.length && lines2[pos2] || '';
+
+  // If the lines match, print l1 and skip l2
+  if (l1 !== '' && l1 === l2) {
+    process.stdout.write(`${l1}\n`);
+    pos1++;
+    pos2++;
+    continue;
+  }
+
+  if (pos2 < lines2.length) {
+    // If l2 is empty, skip l2
+    if (l2 === '') {
+      pos2++;
+      continue;
+    }
+
+    const [l2token] = tokenize(l2);
+
+    // If l2 token matches l1 token, print l1
+    if (pos1 < lines1.length && lines1Tokens[pos1] === l2token) {
+      process.stdout.write(`${l1}\n`);
+      pos1++;
+      pos2++;
+      continue;
+    }
+
+    // If l2 doesn't match any lines in file1, print l2
+    if (l2token && !lines1Tokens.includes(l2token)) {
+      process.stdout.write(`${l2}\n`);
+    }
+    pos2++
+    continue;
+  }
+
+  // If we're not at the end of file1, print l1
+  if (pos1 < lines1.length) {
+    if (pos1 === lines1.length - 1 && l1 === '') {
+      // Don't print tailing newline
+    } else {
+      process.stdout.write(`${l1}\n`);
+    }
+    pos1++;
+  }
+}
diff --git a/scripts/terraform/terraform-docs.sh b/scripts/terraform/terraform-docs.sh
index 7711c48e..446d30d0 100755
--- a/scripts/terraform/terraform-docs.sh
+++ b/scripts/terraform/terraform-docs.sh
@@ -44,7 +44,7 @@ function run-terraform-docs-natively() {
 
 function run-terraform-docs-in-docker() {
 
-    # shellcheck disable=SC1091
+  # shellcheck disable=SC1091
   source ./scripts/docker/docker.lib.sh
   local dir_to_scan="$1"
 

From 00d574b7b5cb2e7a280a3cfb770116425d492482 Mon Sep 17 00:00:00 2001
From: aidenvaines-bjss <aiden.vaines@bjss.com>
Date: Wed, 23 Jul 2025 16:40:10 +0100
Subject: [PATCH 2/4] CCM-11345 Manual Repo Sync

---
 .github/SECURITY.md                   | 4 ++--
 .github/workflows/stage-1-commit.yaml | 2 +-
 LICENCE.md                            | 2 +-
 scripts/config/pre-commit.yaml        | 2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/SECURITY.md b/.github/SECURITY.md
index 241f1e33..0382fd5d 100644
--- a/.github/SECURITY.md
+++ b/.github/SECURITY.md
@@ -21,8 +21,8 @@ If you wish to notify us of a vulnerability via email, please include detailed i
 
 You can reach us at:
 
-- _[ A product team email address ]_
-- [cybersecurity@nhs.net](cybersecurity@nhs.net)
+- [england.nhsnotify@nhs.net](mailto:england.nhsnotify@nhs.net)
+- [cybersecurity@nhs.net](mailto:cybersecurity@nhs.net)
 
 ### NCSC
 
diff --git a/.github/workflows/stage-1-commit.yaml b/.github/workflows/stage-1-commit.yaml
index e56f2f3e..ececcb36 100644
--- a/.github/workflows/stage-1-commit.yaml
+++ b/.github/workflows/stage-1-commit.yaml
@@ -156,7 +156,7 @@ jobs:
       - name: "Checkout code"
         uses: actions/checkout@v4
       - name: "Setup ASDF"
-        uses: asdf-vm/actions/setup@v3
+        uses: asdf-vm/actions/setup@v4
       - name: "Perform Setup"
         uses: ./.github/actions/setup
       - name: "Trivy Scan"
diff --git a/LICENCE.md b/LICENCE.md
index ed56eb21..02174c4c 100644
--- a/LICENCE.md
+++ b/LICENCE.md
@@ -1,6 +1,6 @@
 # MIT Licence
 
-Copyright (c) 2024 Crown Copyright NHS England.
+Copyright (c) 2025 Crown Copyright NHS England.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
diff --git a/scripts/config/pre-commit.yaml b/scripts/config/pre-commit.yaml
index 8843370f..29397e23 100644
--- a/scripts/config/pre-commit.yaml
+++ b/scripts/config/pre-commit.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0 # Use the ref you want to point at
+    rev: v5.0.0 # Use the ref you want to point at
     hooks:
       - id: trailing-whitespace
       - id: detect-aws-credentials

From c1adcd33fe31c6e500305e048719606f88d6efb3 Mon Sep 17 00:00:00 2001
From: aidenvaines-bjss <aiden.vaines@bjss.com>
Date: Thu, 24 Jul 2025 16:45:44 +0100
Subject: [PATCH 3/4] CCM-11345 Manual Repo Sync

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

diff --git a/.github/workflows/scorecard.yml b/.github/workflows/scorecard.yml
index 03bf1714..091fd473 100644
--- a/.github/workflows/scorecard.yml
+++ b/.github/workflows/scorecard.yml
@@ -68,6 +68,6 @@ jobs:
       # Upload the results to GitHub's code scanning dashboard (optional).
       # Commenting out will disable upload of results to your repo's Code Scanning dashboard
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@9e8d0789d4a0fa9ceb6b1738f7e269594bdd67f0 # v3.28.9
+        uses: github/codeql-action/upload-sarif@fca7ace96b7d713c7035871441bd52efbe39e27e # v3.28.19
         with:
           sarif_file: results.sarif

From 31608e8b50b1b15a94d297ad08fe04a36e866458 Mon Sep 17 00:00:00 2001
From: aidenvaines-bjss <aiden.vaines@bjss.com>
Date: Fri, 25 Jul 2025 09:29:45 +0100
Subject: [PATCH 4/4] CCM-11345 Manual Repo Sync

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

diff --git a/.github/workflows/scorecard.yml b/.github/workflows/scorecard.yml
index 091fd473..5552785d 100644
--- a/.github/workflows/scorecard.yml
+++ b/.github/workflows/scorecard.yml
@@ -37,7 +37,7 @@ jobs:
           persist-credentials: false
 
       - name: "Run analysis"
-        uses: ossf/scorecard-action@62b2cac7ed8198b15735ed49ab1e5cf35480ba46 # v2.4.0
+        uses: ossf/scorecard-action@f49aabe0b5af0936a0987cfb85d86b75731b0186 # v2.4.1
         with:
           results_file: results.sarif
           results_format: sarif