diff --git a/.github/workflows/codeql-multiple-repo-scan.yml b/.github/workflows/codeql-multiple-repo-scan.yml
index a22531153b2..cfdb7969791 100644
--- a/.github/workflows/codeql-multiple-repo-scan.yml
+++ b/.github/workflows/codeql-multiple-repo-scan.yml
@@ -24,10 +24,6 @@ on:
   workflow_dispatch:
 permissions:
   contents: write
-# Do not flood CI with unneeded previous runs in PR
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number }}
-  cancel-in-progress: ${{ github.ref_name != 'main' && !startsWith(github.ref_name, 'release/') }}
 jobs:
   analyze-repos:
     name: Analyze Multiple Repositories
@@ -54,11 +50,100 @@ jobs:
       - name: Parse known_good.json and create repos.json
         id: parse-repos
         run: |
-          scripts/workflow/parse_repos.sh
+          sudo apt-get update && sudo apt-get install -y jq
+          JSON_FILE="./known_good.json"
+
+          # Check if the file exists
+          if [ ! -f "$JSON_FILE" ]; then
+            echo "Error file not found '$JSON_FILE' "
+            ls -la .
+            exit 1
+          fi
+
+          # Create repos.json from known_good.json
+          # This jq command transforms the 'modules' object into an array of repository objects
+          # with 'name', 'url', 'version' (branch/tag/hash), and 'path'.
+          jq '[.modules.target_sw | to_entries[] | {
+            name: .key,
+            url: .value.repo,
+            version: (.value.branch // .value.hash // .value.version),
+            path: ("repos/" + .key)
+          }]' "$JSON_FILE" > repos.json
+
+          echo "Generated repos.json:"
+          cat repos.json
+          echo "" # Add a newline for better readability
+
+          # The following GITHUB_OUTPUT variables are set for each module.
+          # These might be useful for other steps, but are not directly used by the 'checkout-repos' step
+          # which now reads 'repos.json' directly.
+          echo "MODULE_COUNT=$(jq '.modules.target_sw | length' "$JSON_FILE")" >> $GITHUB_OUTPUT
+
+          jq -c '.modules.target_sw | to_entries[]' "$JSON_FILE" | while read -r module_entry; do
+            module_name=$(echo "$module_entry" | jq -r '.key')
+            repo_url=$(echo "$module_entry" | jq -r '.value.repo // empty')
+            version=$(echo "$module_entry" | jq -r '.value.version // empty')
+            branch=$(echo "$module_entry" | jq -r '.value.branch // empty')
+            hash=$(echo "$module_entry" | jq -r '.value.hash // empty')
+
+            echo "${module_name}_url=$repo_url" >> $GITHUB_OUTPUT
+
+            if [ -n "$version" ]; then
+             echo "${module_name}_version=$version" >> $GITHUB_OUTPUT
+            fi
+
+            if [ -n "$branch" ]; then
+              echo "${module_name}_branch=$branch" >> $GITHUB_OUTPUT
+            fi
+
+            if [ -n "$hash" ]; then
+              echo "${module_name}_hash=$hash" >> $GITHUB_OUTPUT
+            fi
+          done
       - name: Checkout all pinned repositories
         id: checkout-repos
         run: |
-          scripts/workflow/checkout_repos.sh
+          # jq is already installed by the previous step.
+
+          # Read repositories from the repos.json file created by the previous step
+          repos=$(cat repos.json)
+          repo_count=$(echo "$repos" | jq length)
+
+          # Initialize an empty string for paths to be outputted
+          repo_paths_output=""
+
+          for i in $(seq 0 $((repo_count-1))); do
+            name=$(echo "$repos" | jq -r ".[$i].name")
+            url=$(echo "$repos" | jq -r ".[$i].url")
+            ref=$(echo "$repos" | jq -r ".[$i].version") # This can be a branch, tag, or commit hash
+            path=$(echo "$repos" | jq -r ".[$i].path") # e.g., "repos/score_baselibs"
+
+            echo "Checking out $name ($ref) to $path"
+
+            # Create the parent directory if it doesn't exist
+            mkdir -p "$(dirname "$path")"
+
+            # Check if 'ref' looks like a commit hash (e.g., 40 hex characters)
+            # This is a heuristic; a more robust check might involve fetching refs first.
+            if [[ "$ref" =~ ^[0-9a-fA-F]{40}$ ]]; then
+              echo "  Detected commit hash. Cloning and then checking out."
+              git clone "$url" "$path"
+              (cd "$path" && git checkout "$ref")
+            else
+              echo "  Detected branch/tag. Cloning with --branch."
+              git clone --depth 1 --branch "$ref" "$url" "$path"
+            fi
+
+            # Append the path to the list, separated by commas
+            if [ -z "$repo_paths_output" ]; then
+              repo_paths_output="$path"
+            else
+              repo_paths_output="$repo_paths_output,$path"
+            fi
+          done
+
+          # Output all paths as a single variable
+          echo "repo_paths=$repo_paths_output" >> $GITHUB_OUTPUT
       - name: Initialize CodeQL for all repositories
         uses: github/codeql-action/init@v4
         with:
@@ -75,7 +160,26 @@ jobs:
       - name: Recategorize Guidelines
         if: always()
         run: |
-          scripts/workflow/recategorize_guidelines.sh
+          RECATEGORIZE_SCRIPT="codeql-coding-standards-repo/scripts/guideline_recategorization/recategorize.py"
+          CODING_STANDARDS_CONFIG="./.github/codeql/coding-standards.yml"
+
+          CODING_STANDARDS_SCHEMA="codeql-coding-standards-repo/schemas/coding-standards-schema-1.0.0.json"
+          SARIF_SCHEMA="codeql-coding-standards-repo/schemas/sarif-schema-2.1.0.json"
+
+
+          SARIF_FILE="sarif-results/cpp.sarif"
+
+          mkdir -p sarif-results-recategorized
+          echo "Processing $SARIF_FILE for recategorization..."
+          python3 "$RECATEGORIZE_SCRIPT" \
+            --coding-standards-schema-file "$CODING_STANDARDS_SCHEMA" \
+            --sarif-schema-file "$SARIF_SCHEMA" \
+            "$CODING_STANDARDS_CONFIG" \
+            "$SARIF_FILE" \
+            "sarif-results-recategorized/$(basename "$SARIF_FILE")"
+
+            rm "$SARIF_FILE"
+            mv "sarif-results-recategorized/$(basename "$SARIF_FILE")" "$SARIF_FILE"
       - name: Generate HTML Report from SARIF
         run: |
           SARIF_FILE="sarif-results/cpp.sarif"
diff --git a/scripts/workflow/recategorize_guidelines.sh b/scripts/workflow/recategorize_guidelines.sh
index 8fa4b736020..83d612f70ce 100755
--- a/scripts/workflow/recategorize_guidelines.sh
+++ b/scripts/workflow/recategorize_guidelines.sh
@@ -15,8 +15,9 @@ RECATEGORIZE_SCRIPT="codeql-coding-standards-repo/scripts/guideline_recategoriza
 CODING_STANDARDS_CONFIG="./.github/codeql/coding-standards.yml"
 CODING_STANDARDS_SCHEMA="codeql-coding-standards-repo/schemas/coding-standards-schema-1.0.0.json"
 SARIF_SCHEMA="codeql-coding-standards-repo/schemas/sarif-schema-2.1.0.json"
-SARIF_FILE="sarif-results/cpp.sarif" 
+SARIF_FILE="sarif-results/cpp.sarif"
 mkdir -p sarif-results-recategorized
+
 echo "Processing $SARIF_FILE for recategorization..."
 python3 "$RECATEGORIZE_SCRIPT" \
   --coding-standards-schema-file "$CODING_STANDARDS_SCHEMA" \
@@ -24,5 +25,27 @@ python3 "$RECATEGORIZE_SCRIPT" \
   "$CODING_STANDARDS_CONFIG" \
   "$SARIF_FILE" \
   "sarif-results-recategorized/$(basename "$SARIF_FILE")"
-  rm "$SARIF_FILE"
-  mv "sarif-results-recategorized/$(basename "$SARIF_FILE")" "$SARIF_FILE"
+PY_EXIT=$?
+if [ $PY_EXIT -ne 0 ]; then
+  echo "Recategorization failed (exit code $PY_EXIT). SARIF file not updated." >&2
+  exit $PY_EXIT
+fi
+rm "$SARIF_FILE"
+mv "sarif-results-recategorized/$(basename "$SARIF_FILE")" "$SARIF_FILE"
+
+# # Ensure jq is available
+# if ! command -v jq >/dev/null 2>&1; then
+#   echo "Error: jq is required but not installed. Please install jq and rerun this script." >&2
+#   exit 1
+# fi
+
+# # Filter SARIF to only include results from repos/* (relative or absolute)
+# echo "Filtering SARIF results to only include entries with paths matching (^|/)repos/ ..."
+# jq '(.runs) |= map(.results |= map(select((.locations // [] | length > 0) and ((.locations[0].physicalLocation.artifactLocation.uri // "") | test("(^|/)repos/")))) )' "$SARIF_FILE" > "${SARIF_FILE}.filtered"
+# if [ $? -eq 0 ]; then
+#   mv "${SARIF_FILE}.filtered" "$SARIF_FILE"
+# else
+#   echo "jq filtering failed. SARIF file was not modified." >&2
+#   rm -f "${SARIF_FILE}.filtered"
+#   exit 1
+# fi