diff --git a/.gitattributes b/.gitattributes
index 5378fe089b..5b82ef218b 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1 +1,4 @@
-* -text
\ No newline at end of file
+* -text
+
+# Explicitly ensure shell scripts use LF for CI compatibility
+*.sh text eol=lf
\ No newline at end of file
diff --git a/.github/scripts/clang-query.sh b/.github/scripts/clang-query.sh
new file mode 100644
index 0000000000..7ccc6b723f
--- /dev/null
+++ b/.github/scripts/clang-query.sh
@@ -0,0 +1,202 @@
+#!/usr/bin/env bash
+set -e
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
+TMP_DIR="$REPO_ROOT/.ci_tmp"
+mkdir -p "$TMP_DIR"
+
+# Define the cleanup function
+cleanup() {
+    echo "Cleaning up temporary files..."
+    rm -rf "$TMP_DIR"
+}
+
+# Register the trap: run cleanup on EXIT, plus common signals like INT (Ctrl+C) or TERM
+# trap cleanup EXIT INT TERM
+
+
+cd "$REPO_ROOT"
+
+# find path to compile_commands.json
+if [ -f "$REPO_ROOT/SerialPrograms/bin/compile_commands.json" ]; then
+    DB_PATH="$REPO_ROOT/SerialPrograms/bin/compile_commands.json"
+elif [ -f "$REPO_ROOT/build/RelWithDebInfo/compile_commands.json" ]; then
+    DB_PATH="$REPO_ROOT/build/RelWithDebInfo/compile_commands.json"
+else
+    echo "Error: compile_commands.json not found!"
+    exit 1
+fi
+
+
+echo "Generating clang-scan-deps experimental-full > deps.json."
+
+# in ubuntu, the command is clang-scan-deps-18. in Windows, it is clang-scan-deps
+SCAN_DEPS=$(command -v clang-scan-deps-18 || command -v clang-scan-deps)
+
+# Safety check: Exit if the tool isn't found
+if [ -z "$SCAN_DEPS" ]; then
+  echo "Error: clang-scan-deps (or version -18) not found in PATH."
+  exit 1
+fi
+
+
+# filter compile_commands.json, to remove .rc files, since clang-scan-deps doesn't recognize this format
+jq '[.[] | select(.file | endswith(".rc") | not)]' "$DB_PATH" > "$TMP_DIR/compile_commands_filtered.json"
+
+# get dependency graph
+"$SCAN_DEPS" -compilation-database "$TMP_DIR/compile_commands_filtered.json" -format experimental-full > "$TMP_DIR/deps.json"
+
+# normalize slashes
+# sed 's|\\\\|/|g' deps.json > normalized_deps.json
+sed -i 's|\\\\|/|g' "$TMP_DIR/deps.json"
+
+# check if deps.json has the expected keys
+# because we are relying on clang-scan-deps experimental-full, where the names of the keys can change.
+TU_KEY="translation-units"
+CMD_KEY="commands"
+DEPS="file-deps"
+INPUT="input-file"
+
+JQ_SCRIPT=$(cat << 'EOF'
+	# 1. Access the target object
+  (.[$TU][0][$CMD][0]) as $target
+  
+  # 2. Define the required keys
+
+  | [$DEPS, $INPUT] as $required
+
+  | (
+	if .[$TU] == null then 
+		"Missing: \($TU). Keys found at top-level: \(keys_unsorted)"
+	elif .[$TU][0] == null then 
+		"Missing: \($TU)[0]"
+	elif .[$TU][0].[$CMD] == null then 
+		"Missing: \($TU)[0].\($CMD). Keys found from \($TU)[0]: \(.[$TU][0] | keys_unsorted)"
+	elif $target == null then 
+		"Missing: \($TU)[0].[$CMD][0]"
+	elif ($required | all(. as $req | $target | has($req)) | not) then
+	  "Missing: One or more required keys \($required). Found: \($target | keys_unsorted)"
+	# elif (.[$TU][0].[$CMD][0] | keys_unsorted | any(. == [$DEPS] or . == [$INPUT]) | not) then
+	#     "Missing: both \($DEPS) and \($INPUT). Found: \(.[$TU][0][$CMD][0] | keys_unsorted)"
+	else 
+	  "All keys \($required) found in \($TU)[0].\($CMD)[0]"
+	end
+  ) as $result
+
+  | if ($result | type == "string" and startswith("Missing:")) then 
+		("\($result). The keys within the experimental-full format from clang-scan-deps can change over time. Please fix the CI to use the correct keys.") | halt_error
+		else $result end
+EOF
+)
+
+echo "Checking keys in deps.json."
+jq -r "$JQ_SCRIPT" \
+	--arg TU "$TU_KEY" \
+	--arg CMD "$CMD_KEY" \
+	--arg DEPS "$DEPS" \
+	--arg INPUT "$INPUT" \
+	"$TMP_DIR/deps.json"
+
+echo "Generating changed_files.txt from git diff."
+
+# git diff with relative paths
+git diff --name-only origin/main...HEAD > "$TMP_DIR/changed_files.txt"
+
+echo "Generating files_to_query.txt, based on changed_files.txt and deps.json."
+
+# for each line in changed_files_unix.txt, search deps.json to find all their dependants
+jq -r --rawfile mod "$TMP_DIR/changed_files.txt" \
+	--arg TU "$TU_KEY" \
+	--arg CMD "$CMD_KEY" \
+	--arg DEPS "$DEPS" \
+	--arg INPUT "$INPUT" '
+  # 1. Clean the list of changed files
+  ($mod | split("\n") | map(select(length > 0))) as $changes |
+  
+  # 2. Access the translation-units array
+  [ .[$TU][] | .[$CMD][] | 
+	select(
+	  # 3. Check "file-deps" for matches
+	  .[$DEPS][] | . as $dp | 
+	  any($changes[]; . as $c | $dp | endswith($c))
+	) | 
+	# 4. Get the source file path
+	.[$INPUT] 
+  ] | unique[]
+' "$TMP_DIR/deps.json" | tr -d '\r' > "$TMP_DIR/files_to_query.txt"
+
+
+
+cat << 'EOF' > "$TMP_DIR/query.txt"
+set output dump
+match invocation(
+  isExpansionInFileMatching("SerialPrograms/"),
+  hasDeclaration(cxxConstructorDecl(ofClass(hasName("std::filesystem::path")))),
+  hasArgument(0, hasType(asString("std::string")))
+)
+EOF
+
+echo "Running clang-query."
+
+# files=$(jq -r '.[].file' "$DB_PATH")
+DB_DIR=$(dirname "$DB_PATH")
+#echo "$files" | xargs --max-args=150 clang-query -p "$DB_DIR" -f "$TMP_DIR/query.txt" >> output.txt
+
+# jq -r '.[].file' "$DB_PATH" | sed 's/\\/\//g' | tr -d '\r'  | xargs -d '\n' --max-args=150 clang-query -p "$DB_DIR" -f "$TMP_DIR/query.txt" -- -Wno-unused-command-line-argument >> "$TMP_DIR/output.txt"
+
+# this works
+# jq -r '.[].file' "$DB_PATH" | sed 's/\\/\//g' | tr -d '\r'  | xargs -d '\n' --max-args=150 clang-query -p "$DB_DIR" -f "$TMP_DIR/query.txt" >> "$TMP_DIR/output.txt"
+# jq -r '.[].file' "$DB_PATH" | tr -d '\r'  | xargs -d '\n' --max-args=150 clang-query -p "$DB_DIR" -f "$TMP_DIR/query.txt" >> "$TMP_DIR/output.txt"
+
+# also works
+# jq -r '.[].file' "$DB_PATH" | tr -d '\r' | xargs -d '\n' --max-args=150 \
+# clang-query -p "$DB_DIR" \
+# --extra-arg="-Wno-unused-command-line-argument" \
+# -f "$TMP_DIR/query.txt" >> "$TMP_DIR/output.txt"
+
+# also works
+# jq -r '.[].file' "$DB_PATH" | tr -d '\r' | sed 's|\\|/|g' | \
+# 	xargs -d '\n' --max-args=150 \
+# 	clang-query -p "$DB_DIR" \
+# 	--extra-arg="-Wno-unused-command-line-argument" \
+# 	--extra-arg="-Wno-unused-function" \
+# 	-f "$TMP_DIR/query.txt" >> "$TMP_DIR/output.txt"
+
+# in ubuntu, the command is clang-query-18. in Windows, it is clang-query
+CLANG_QUERY=$(command -v clang-query-18 || command -v clang-query)
+
+if [ -z "$CLANG_QUERY" ]; then
+    echo "Error: clang-query (or version -18) not found!"
+    exit 1
+fi
+
+ONLY_CHECK_CHANGED_FILES=true
+if [ "$ONLY_CHECK_CHANGED_FILES" = "true" ]; then
+    LIST_FILE="$TMP_DIR/files_to_query.txt"
+else # check all files
+	LIST_FILE="$TMP_DIR/file_list.txt"
+    jq -r '.[].file' "$DB_PATH" | tr -d '\r' | sed 's|\\|/|g' > "$LIST_FILE"
+fi
+
+> "$TMP_DIR/output.txt"
+
+# Run clang-query using the list file
+# check if LIST_FILE has any data to analyze
+if [ ! -s "$LIST_FILE" ]; then
+    echo "No files found to analyze. Skipping Clang-Query."
+else
+    xargs -d '\n' -a "$LIST_FILE" --max-args=150 \
+		"$CLANG_QUERY" -p "$DB_DIR" \
+		--extra-arg="-Wno-unused-command-line-argument" \
+		--extra-arg="-Wno-unused-function" \
+		-f "$TMP_DIR/query.txt" >> "$TMP_DIR/output.txt"
+fi
+
+
+
+cat "$TMP_DIR/output.txt"
+if grep --silent "Match #" "$TMP_DIR/output.txt"; then
+  echo "::error Forbidden std::filesystem::path construction detected!"
+  exit 1
+fi
\ No newline at end of file
diff --git a/.github/workflows/cpp-ci-serial-programs-base.yml b/.github/workflows/cpp-ci-serial-programs-base.yml
index 09d52a5ba1..bb59444045 100644
--- a/.github/workflows/cpp-ci-serial-programs-base.yml
+++ b/.github/workflows/cpp-ci-serial-programs-base.yml
@@ -51,6 +51,8 @@ jobs:
       with:
         path: 'Arduino-Source'
         submodules: 'recursive'
+        fetch-depth: 0
+        filter: blob:none
 
     - name: Install Qt
       uses: jurplel/install-qt-action@v4
@@ -64,7 +66,7 @@ jobs:
         cd Arduino-Source
         sudo apt update
         sudo apt upgrade
-        sudo apt install clang-tools libopencv-dev
+        sudo apt install clang-tools-18 libopencv-dev
 
         sudo apt install ./3rdPartyBinaries/libdpp-10.0.28-linux-x64.deb
 
@@ -88,6 +90,25 @@ jobs:
         cmake .. -DQT_MAJOR:STRING=6 ${{env.CMAKE_ADDITIONAL_FLAGS}}
         cmake --build . --config RelWithDebInfo --parallel 10
 
+    # - name: Fake missing Qt generated files (for testing clang-query without building the whole project)
+    #   if: inputs.run-clang-query
+    #   run: |
+    #     # Create the bin directory if it doesn't exist
+    #     mkdir -p Arduino-Source/SerialPrograms/bin
+        
+    #     # Fake the RCC (resource) files
+    #     touch Arduino-Source/SerialPrograms/bin/qrc_darkstyle.cpp
+        
+    #     # Fake the MOC/Autogen files for all components
+    #     mkdir -p Arduino-Source/SerialPrograms/bin/SerialProgramsLib_autogen
+    #     touch Arduino-Source/SerialPrograms/bin/SerialProgramsLib_autogen/mocs_compilation.cpp
+        
+    #     mkdir -p Arduino-Source/SerialPrograms/bin/SerialPrograms_autogen
+    #     touch Arduino-Source/SerialPrograms/bin/SerialPrograms_autogen/mocs_compilation.cpp
+        
+    #     mkdir -p Arduino-Source/SerialPrograms/bin/SerialProgramsCommandLine_autogen
+    #     touch Arduino-Source/SerialPrograms/bin/SerialProgramsCommandLine_autogen/mocs_compilation.cpp
+
     - name: Prepare upload build
       if: inputs.upload-build
       shell: bash
@@ -128,22 +149,6 @@ jobs:
 
     - name: Run clang query
       if: inputs.run-clang-query
-      run : |
-        cd Arduino-Source
-
-        cat << 'EOF' > query.txt
-        set output dump
-        match invocation(
-          isExpansionInFileMatching("SerialPrograms/"),
-          hasDeclaration(cxxConstructorDecl(ofClass(hasName("std::filesystem::path")))),
-          hasArgument(0, hasType(asString("std::string")))
-        )
-        EOF
-
-        files=$(jq -r '.[].file' SerialPrograms/bin/compile_commands.json)
-        echo "$files" | xargs --max-args=150 clang-query -p SerialPrograms/bin/ -f query.txt >> output.txt
-        cat output.txt
-        if grep --silent "Match #" output.txt; then
-          echo "::error Forbidden std::filesystem::path construction detected!"
-          exit 1
-        fi
+      working-directory: ./Arduino-Source
+      run : bash ./.github/scripts/clang-query.sh
+        
diff --git a/.gitignore b/.gitignore
index f5a66a76bd..a75814b851 100644
--- a/.gitignore
+++ b/.gitignore
@@ -75,3 +75,5 @@ build_*/
 .cache/*
 Packages/*
 
+.ci_tmp
+