diff --git a/scripts/ci/binary-artifacts.sh b/scripts/ci/binary-artifacts.sh
index 4d420eb9aa..4d63a71e2a 100755
--- a/scripts/ci/binary-artifacts.sh
+++ b/scripts/ci/binary-artifacts.sh
@@ -30,12 +30,12 @@ set -euo pipefail
 #   - WebAssembly modules, compiled Java classes, .NET assemblies
 #
 # Runs in two contexts:
-#   pre-commit hook  -- checks staged files   (--check --staged)
+#   pre-commit hook  -- checks filenames passed by pre-commit (--check files...)
 #   CI workflow      -- checks PR diff files  (--check --ci)
 #
 # Exit codes: 0 = clean, 1 = binary artifacts found or error.
 
-FILE_MODE="staged"
+FILE_MODE="all"
 FILES=()
 
 while [[ $# -gt 0 ]]; do
@@ -43,25 +43,16 @@ while [[ $# -gt 0 ]]; do
     --check)
       shift
       ;;
-    --staged)
-      FILE_MODE="staged"
-      shift
-      ;;
     --ci)
       FILE_MODE="ci"
       shift
       ;;
-    --all)
-      FILE_MODE="all"
-      shift
-      ;;
     --help|-h)
-      echo "Usage: $0 [--check] [--staged|--ci|--all] [files...]"
+      echo "Usage: $0 [--check] [--ci] [files...]"
       echo ""
       echo "File selection:"
-      echo "  --staged  Check staged files (default, for git hooks)"
+      echo "  [none]    Check all tracked files (default)"
       echo "  --ci      Check files changed in PR (for CI)"
-      echo "  --all     Check all tracked files"
       echo "  [files]   Check specific files"
       exit 0
       ;;
@@ -79,9 +70,6 @@ done
 
 get_files() {
   case "$FILE_MODE" in
-    staged)
-      git diff --cached --name-only --diff-filter=ACM
-      ;;
     ci)
       if [ -n "${GITHUB_BASE_REF:-}" ]; then
         git fetch --no-tags --depth=1 origin "${GITHUB_BASE_REF}:${GITHUB_BASE_REF}" 2>/dev/null || true
@@ -89,7 +77,7 @@ get_files() {
       elif [ -n "${CI:-}" ]; then
         git diff --name-only --diff-filter=ACM HEAD~1
       else
-        git diff --cached --name-only --diff-filter=ACM
+        git ls-files
       fi
       ;;
     all)
diff --git a/scripts/ci/markdownlint.sh b/scripts/ci/markdownlint.sh
index 0db7dfdb31..a937956e4e 100755
--- a/scripts/ci/markdownlint.sh
+++ b/scripts/ci/markdownlint.sh
@@ -19,11 +19,10 @@
 set -euo pipefail
 
 MODE="check"
-FILE_MODE="all"
 FILES=()
 
-# Accept mode flags plus optional file paths. In pre-commit, matching staged
-# markdown files are passed as positional arguments.
+# Accept mode flags plus optional file paths. Pre-commit passes matching
+# markdown files as positional arguments.
 while [[ $# -gt 0 ]]; do
   case "$1" in
     --check)
@@ -34,20 +33,10 @@ while [[ $# -gt 0 ]]; do
       MODE="fix"
       shift
       ;;
-    --staged)
-      FILE_MODE="staged"
-      shift
-      ;;
-    --all)
-      FILE_MODE="all"
-      shift
-      ;;
     --help|-h)
-      echo "Usage: $0 [--check|--fix] [--staged|--all] [files...]"
+      echo "Usage: $0 [--check|--fix] [files...]"
       echo "  --check   Check markdown files for issues (default)"
       echo "  --fix     Automatically fix markdown issues"
-      echo "  --staged  Check staged markdown files"
-      echo "  --all     Check all markdown files (default)"
       exit 0
       ;;
     -*)
@@ -66,19 +55,6 @@ done
 # helm/charts/iggy/README.md is auto-generated by helm-docs
 IGNORE_ARGS=(--ignore "helm/charts/iggy/README.md")
 
-# Keep --staged for manual runs; pre-commit normally passes matching staged
-# files directly through pass_filenames.
-if [ ${#FILES[@]} -eq 0 ] && [ "$FILE_MODE" = "staged" ]; then
-  while IFS= read -r file; do
-    [ -n "$file" ] && FILES+=("$file")
-  done < <(git diff --cached --name-only --diff-filter=ACM -- '*.md')
-
-  if [ ${#FILES[@]} -eq 0 ]; then
-    echo "✅ No staged markdown files to check"
-    exit 0
-  fi
-fi
-
 # Default to the full repository for CI/manual runs, but use the explicit file
 # list when pre-commit or a caller passes paths directly.
 if [ ${#FILES[@]} -gt 0 ]; then
diff --git a/scripts/ci/shellcheck.sh b/scripts/ci/shellcheck.sh
index 4f66fdbca0..1cc970c452 100755
--- a/scripts/ci/shellcheck.sh
+++ b/scripts/ci/shellcheck.sh
@@ -21,11 +21,10 @@
 set -euo pipefail
 
 MODE="check"
-FILE_MODE="all"
 FILES=()
 
-# Accept mode flags plus optional file paths. In pre-commit, matching staged
-# shell files are passed as positional arguments.
+# Accept mode flags plus optional file paths. Pre-commit passes matching shell
+# files as positional arguments.
 while [[ $# -gt 0 ]]; do
   case "$1" in
     --check)
@@ -36,20 +35,10 @@ while [[ $# -gt 0 ]]; do
       MODE="fix"
       shift
       ;;
-    --staged)
-      FILE_MODE="staged"
-      shift
-      ;;
-    --all)
-      FILE_MODE="all"
-      shift
-      ;;
     --help|-h)
-      echo "Usage: $0 [--check|--fix] [--staged|--all] [files...]"
+      echo "Usage: $0 [--check|--fix] [files...]"
       echo "  --check   Check shell scripts for issues (default)"
       echo "  --fix     Show detailed suggestions for fixes"
-      echo "  --staged  Check staged shell scripts"
-      echo "  --all     Check all shell scripts (default)"
       exit 0
       ;;
     -*)
@@ -88,26 +77,6 @@ for path in "${EXCLUDE_PATHS[@]}"; do
   FIND_EXCLUDE_ARGS+=("-not" "-path" "$path")
 done
 
-# Keep --staged for manual runs; pre-commit normally passes matching staged
-# files directly through pass_filenames.
-if [ ${#FILES[@]} -eq 0 ] && [ "$FILE_MODE" = "staged" ]; then
-  while IFS= read -r script; do
-    if [ ! -f "$script" ]; then
-      continue
-    fi
-
-    # Match normal .sh files and executable scripts with shell shebangs.
-    if [[ "$script" == *.sh ]] || head -n 1 "$script" | grep -qE '^#!.*[^[:alnum:]_](bash|dash|ksh|zsh|sh)([[:space:]]|$)'; then
-      FILES+=("$script")
-    fi
-  done < <(git diff --cached --name-only --diff-filter=ACM)
-
-  if [ ${#FILES[@]} -eq 0 ]; then
-    echo "✅ No staged shell scripts to check"
-    exit 0
-  fi
-fi
-
 # Check if shellcheck is installed
 if ! command -v shellcheck &> /dev/null; then
   echo "❌ shellcheck command not found"
@@ -128,8 +97,8 @@ if [ "$MODE" = "fix" ]; then
   echo ""
 
   FAILED=0
-  # Use staged or explicitly provided files when present; otherwise keep the
-  # historical full-repository behavior for CI/manual all-file checks.
+  # Use file arguments from pre-commit or the caller when present; otherwise
+  # keep the historical full-repository behavior for CI/manual checks.
   if [ ${#FILES[@]} -gt 0 ]; then
     for script in "${FILES[@]}"; do
       [ -f "$script" ] || continue
@@ -159,8 +128,8 @@ if [ "$MODE" = "fix" ]; then
 else
   echo "🔍 Checking shell scripts..."
 
-  # Use staged or explicitly provided files when present; otherwise keep the
-  # historical full-repository behavior for CI/manual all-file checks.
+  # Use file arguments from pre-commit or the caller when present; otherwise
+  # keep the historical full-repository behavior for CI/manual checks.
   if [ ${#FILES[@]} -gt 0 ]; then
     if shellcheck -x "${FILES[@]}"; then
       echo "✅ All shell scripts passed shellcheck"
diff --git a/scripts/ci/taplo.sh b/scripts/ci/taplo.sh
index 7240368c2d..1568d17d93 100755
--- a/scripts/ci/taplo.sh
+++ b/scripts/ci/taplo.sh
@@ -20,7 +20,7 @@ set -euo pipefail
 
 # Default values
 MODE="check"
-FILE_MODE="staged"
+FILE_MODE="all"
 FILES=()
 
 # Parse arguments
@@ -34,29 +34,20 @@ while [[ $# -gt 0 ]]; do
       MODE="fix"
       shift
       ;;
-    --staged)
-      FILE_MODE="staged"
-      shift
-      ;;
     --ci)
       FILE_MODE="ci"
       shift
       ;;
-    --all)
-      FILE_MODE="all"
-      shift
-      ;;
     --help|-h)
-      echo "Usage: $0 [--check|--fix] [--staged|--ci|--all] [files...]"
+      echo "Usage: $0 [--check|--fix] [--ci] [files...]"
       echo ""
       echo "Modes:"
       echo "  --check   Check TOML formatting (default)"
       echo "  --fix     Format TOML files"
       echo ""
       echo "File selection:"
-      echo "  --staged  Check staged files (default, for git hooks)"
+      echo "  [none]    Check all tracked TOML files (default)"
       echo "  --ci      Check files changed in PR (for CI)"
-      echo "  --all     Check all TOML files"
       echo "  [files]   Check specific files"
       exit 0
       ;;
@@ -87,10 +78,6 @@ fi
 # Get files to check based on mode
 get_files() {
   case "$FILE_MODE" in
-    staged)
-      # Get staged TOML files for git hooks
-      git diff --cached --name-only --diff-filter=ACM -- '*.toml'
-      ;;
     ci)
       # Get TOML files changed in PR for CI
       if [ -n "${GITHUB_BASE_REF:-}" ]; then
@@ -101,18 +88,13 @@ get_files() {
         # Generic CI - compare with HEAD~1
         git diff --name-only --diff-filter=ACM HEAD~1 -- '*.toml'
       else
-        # Fallback to staged files
-        git diff --cached --name-only --diff-filter=ACM -- '*.toml'
+        # Local fallback: check all tracked TOML files
+        git ls-files -- '*.toml'
       fi
       ;;
     all)
       # Get all TOML files (excluding common build directories)
-      find . -name '*.toml' \
-        -not -path './target/*' \
-        -not -path './node_modules/*' \
-        -not -path './.git/*' \
-        -not -path './venv/*' \
-        -type f
+      git ls-files -- '*.toml'
       ;;
   esac
 }
diff --git a/scripts/ci/trailing-newline.sh b/scripts/ci/trailing-newline.sh
index bbab2e564c..107d51b61d 100755
--- a/scripts/ci/trailing-newline.sh
+++ b/scripts/ci/trailing-newline.sh
@@ -20,7 +20,7 @@ set -euo pipefail
 
 # Default values
 MODE="check"
-FILE_MODE="staged"
+FILE_MODE="all"
 FILES=()
 
 # Parse arguments
@@ -34,29 +34,20 @@ while [[ $# -gt 0 ]]; do
       MODE="fix"
       shift
       ;;
-    --staged)
-      FILE_MODE="staged"
-      shift
-      ;;
     --ci)
       FILE_MODE="ci"
       shift
       ;;
-    --all)
-      FILE_MODE="all"
-      shift
-      ;;
     --help|-h)
-      echo "Usage: $0 [--check|--fix] [--staged|--ci|--all] [files...]"
+      echo "Usage: $0 [--check|--fix] [--ci] [files...]"
       echo ""
       echo "Modes:"
       echo "  --check   Check for missing trailing newlines (default)"
       echo "  --fix     Add trailing newlines to files"
       echo ""
       echo "File selection:"
-      echo "  --staged  Check staged files (default, for git hooks)"
+      echo "  [none]    Check all tracked files (default)"
       echo "  --ci      Check files changed in PR (for CI)"
-      echo "  --all     Check all tracked files"
       echo "  [files]   Check specific files"
       exit 0
       ;;
@@ -76,10 +67,6 @@ done
 # Get files to check based on mode
 get_files() {
   case "$FILE_MODE" in
-    staged)
-      # Get staged files for git hooks
-      git diff --cached --name-only --diff-filter=ACM
-      ;;
     ci)
       # Get files changed in PR for CI
       if [ -n "${GITHUB_BASE_REF:-}" ]; then
@@ -90,8 +77,8 @@ get_files() {
         # Generic CI - compare with HEAD~1
         git diff --name-only --diff-filter=ACM HEAD~1
       else
-        # Fallback to staged files
-        git diff --cached --name-only --diff-filter=ACM
+        # Local fallback: check all tracked files
+        git ls-files
       fi
       ;;
     all)
diff --git a/scripts/ci/trailing-whitespace.sh b/scripts/ci/trailing-whitespace.sh
index 4e7f2410d3..34bc0f8776 100755
--- a/scripts/ci/trailing-whitespace.sh
+++ b/scripts/ci/trailing-whitespace.sh
@@ -20,7 +20,7 @@ set -euo pipefail
 
 # Default values
 MODE="check"
-FILE_MODE="staged"
+FILE_MODE="all"
 FILES=()
 
 # Parse arguments
@@ -34,29 +34,20 @@ while [[ $# -gt 0 ]]; do
       MODE="fix"
       shift
       ;;
-    --staged)
-      FILE_MODE="staged"
-      shift
-      ;;
     --ci)
       FILE_MODE="ci"
       shift
       ;;
-    --all)
-      FILE_MODE="all"
-      shift
-      ;;
     --help|-h)
-      echo "Usage: $0 [--check|--fix] [--staged|--ci|--all] [files...]"
+      echo "Usage: $0 [--check|--fix] [--ci] [files...]"
       echo ""
       echo "Modes:"
       echo "  --check   Check for trailing whitespace (default)"
       echo "  --fix     Remove trailing whitespace"
       echo ""
       echo "File selection:"
-      echo "  --staged  Check staged files (default, for git hooks)"
+      echo "  [none]    Check all tracked files (default)"
       echo "  --ci      Check files changed in PR (for CI)"
-      echo "  --all     Check all tracked files"
       echo "  [files]   Check specific files"
       exit 0
       ;;
@@ -76,10 +67,6 @@ done
 # Get files to check based on mode
 get_files() {
   case "$FILE_MODE" in
-    staged)
-      # Get staged files for git hooks
-      git diff --cached --name-only --diff-filter=ACM
-      ;;
     ci)
       # Get files changed in PR for CI
       if [ -n "${GITHUB_BASE_REF:-}" ]; then
@@ -90,8 +77,8 @@ get_files() {
         # Generic CI - compare with HEAD~1
         git diff --name-only --diff-filter=ACM HEAD~1
       else
-        # Fallback to staged files
-        git diff --cached --name-only --diff-filter=ACM
+        # Local fallback: check all tracked files
+        git ls-files
       fi
       ;;
     all)