fix(lint): fix all sonarcloud detected issues (#279)

* fix(ci): replace broad permissions with specific scopes in workflows Replace read-all/write-all with minimum required permission scopes across all GitHub Actions workflows to follow the principle of least privilege (SonarCloud rule githubactions:S8234). * fix(shell): use [[ instead of [ for conditional tests Replace single brackets with double brackets in bash conditional expressions across 14 files (28 changes). All scripts use bash shebangs so [[ is safe everywhere (SonarCloud rule shelldre:S7688). * fix(shell): add explicit return statements to functions Add return 0 as the last statement in ~46 shell functions across 17 files that previously relied on implicit return codes (SonarCloud rule shelldre:S7682). * fix(shell): assign positional parameters to local variables Replace direct $1/$2/$3 usage with named local variables in _log(), msg(), msg_err(), msg_done(), msg_run(), msg_ok(), and array_diff() (SonarCloud rule shelldre:S7679). * fix(python): replace dict() constructor with literal Use {} instead of dict() for empty dictionary initialization (SonarCloud rule python:S7498). * fix(shell): fix husky shebang and tolerate npm outdated exit code * docs(shell): add function docstring comments * fix(shell): fix heredoc indentation in x-sonarcloud * feat(python): add ruff linter and formatter configuration * fix(ci): align megalinter config with biome, ruff, and shfmt settings * fix(ci): disable black and yaml-prettier in megalinter config * chore(ci): update ruff-pre-commit to v0.15.0 and fix hook name * fix(scripts): check for .git dir before skipping clone in install-fonts * fix(shell): address code review issues in scripts and shared.sh - Guard wezterm show-keys failure in create-wezterm-keymaps.sh - Stop masking git failures with return 0 in install-cheat-purebashbible.sh - Add missing shared.sh source in install-xcode-cli-tools.sh - Replace exit 1 with return 1 in sourced shared.sh * fix(scripts): address code review and security findings - Guard wezterm show-keys failure in create-wezterm-keymaps.sh - Stop masking git failures with return 0 in install-cheat-purebashbible.sh - Add missing shared.sh source in install-xcode-cli-tools.sh - Replace exit 1 with return 1 in sourced shared.sh - Remove shell=True subprocess calls in x-git-largest-files.py * style(shell): apply shfmt formatting and add args to pre-commit hook * fix(python): suppress bandit false positives in x-git-largest-files * fix(python): add nosemgrep suppression for check_output call * feat(format): add prettier for YAML formatting Install prettier, add .prettierrc.json config (200-char width, 2-space indent, LF endings), .prettierignore, yarn scripts (lint:prettier, fix:prettier, format:yaml), and pre-commit hook scoped to YAML files. * style(yaml): apply prettier formatting * fix(scripts): address remaining code review findings - Python: use list comprehension to filter empty strings instead of slicing off the last element - create-wezterm-keymaps: write to temp file and mv for atomic updates - install-xcode-cli-tools: fix shellcheck source directive path * fix(python): sort imports alphabetically in x-git-largest-files * fix(lint): disable PYTHON_ISORT in MegaLinter, ruff handles it * chore(git): add __pycache__ to gitignore * fix(python): rename ambiguous variable l to line (E741) * style: remove trailing whitespace and blank lines * style(fzf): apply shfmt formatting * style(shell): apply shfmt formatting * docs(plans): add design documents * style(docs): add language specifier to fenced code block * feat(lint): add markdown-table-formatter to dev tooling Add markdown-table-formatter as a dev dependency with yarn scripts (lint:md-table, fix:md-table) and a local pre-commit hook to automatically format markdown tables on commit.
2026-02-08 07:50:53 +00:00 · 2026-02-07 19:01:02 +02:00
parent cff3d1dd8a
commit 6d72003446
86 changed files with 1264 additions and 425 deletions
--- a/local/bin/README.md
+++ b/local/bin/README.md
@@ -20,7 +20,7 @@ Some problematic code has been fixed per `shellcheck` suggestions.
 ## Sourced

 | Script                  | Source            |
-| ----------------------- | ----------------- |
+|-------------------------|-------------------|
 | `x-dupes`               | skx/sysadmin-util |
 | `x-foreach`             | mvdan/dotfiles    |
 | `x-multi-ping`          | skx/sysadmin-util |
--- a/local/bin/dfm
+++ b/local/bin/dfm
@@ -64,6 +64,7 @@ menu_builder()
  done
 }

+# Handle install section commands
 section_install()
 {
  USAGE_PREFIX="$SCRIPT install <command>"
@@ -193,6 +194,7 @@ section_install()
  esac
 }

+# Handle Homebrew section commands
 section_brew()
 {
  USAGE_PREFIX="$SCRIPT brew <command>"
@@ -291,6 +293,7 @@ section_brew()
  esac
 }

+# Handle helper utility commands
 section_helpers()
 {
  USAGE_PREFIX="$SCRIPT helpers <command>"
@@ -367,6 +370,7 @@ section_helpers()
  esac
 }

+# Handle apt package manager commands
 section_apt()
 {
  USAGE_PREFIX="$SCRIPT apt <command>"
@@ -435,6 +439,7 @@ section_apt()
  esac
 }

+# Handle documentation generation commands
 section_docs()
 {
  USAGE_PREFIX="$SCRIPT docs <command>"
@@ -459,6 +464,7 @@ section_docs()
  esac
 }

+# Handle dotfiles formatting and reset commands
 section_dotfiles()
 {
  USAGE_PREFIX="$SCRIPT dotfiles <command>"
@@ -526,6 +532,7 @@ section_dotfiles()
  esac
 }

+# Handle system check commands (arch, hostname)
 section_check()
 {
  USAGE_PREFIX="$SCRIPT check <command>"
@@ -552,6 +559,7 @@ section_check()
  esac
 }

+# Handle install script execution
 section_scripts()
 {
  USAGE_PREFIX="$SCRIPT scripts <command>"
@@ -619,6 +627,7 @@ section_tests()
  esac
 }

+# Display main usage information for all sections
 usage()
 {
  echo ""
@@ -642,6 +651,7 @@ usage()
  section_helpers
 }

+# Parse section argument and dispatch to handler
 main()
 {
  SECTION="${1:-}"
--- a/local/bin/git-attributes
+++ b/local/bin/git-attributes
@@ -22,32 +22,37 @@ if [ "$DEBUG" -eq 1 ]; then
  set -x
 fi

-# Output functions
+# Print an error message in red
 msg_err()
 {
  echo -e "\e[31m$*\e[0m" >&2
 }

+# Print a success message in green
 msg_success()
 {
  echo -e "\e[32m$*\e[0m"
 }

+# Print a warning message in yellow
 msg_warn()
 {
  echo -e "\e[33m$*\e[0m" >&2
 }

+# Print an info message in blue
 msg_info()
 {
  echo -e "\e[36m$*\e[0m"
 }

+# Print a debug message when verbose mode is on
 msg_debug()
 {
  [[ $VERBOSE -eq 1 ]] && echo -e "\e[35m$*\e[0m"
 }

+# Display usage information and examples
 show_help()
 {
  cat << EOF
--- a/local/bin/git-dirty
+++ b/local/bin/git-dirty
@@ -90,13 +90,14 @@ declare -A DIR_HAS_REPOS
 # Record start time
 START_TIME=$(date +%s)

-# Logging functions
+# Log an error message
 log_error()
 {
  print_color "31" "ERROR:" >&2
  echo " $*" >&2
 }

+# Log an informational message
 log_info()
 {
  if [[ $VERBOSE -eq 1 ]]; then
@@ -105,6 +106,7 @@ log_info()
  fi
 }

+# Log a warning message
 log_warn()
 {
  print_color "33" "WARNING:" >&2
@@ -911,6 +913,7 @@ process_in_parallel()
  echo -e "\nProcessed $total repositories in $dur (Total runtime: $runtime)"
 }

+# Check a directory for git status with progress tracking
 check_directory_with_progress()
 {
  local dir
--- a/local/bin/msgr
+++ b/local/bin/msgr
@@ -23,21 +23,25 @@ CLR_RESET="\033[0m"
 #  │ Color functions                                          │
 #  ╰──────────────────────────────────────────────────────────╯

+# Wrap text in red color
 function __color_red()
 {
  local MSG="$1"
  echo -e "${CLR_RED}${MSG}${CLR_RESET}"
 }
+# Wrap text in yellow color
 function __color_yellow()
 {
  local MSG="$1"
  echo -e "${CLR_YELLOW}${MSG}${CLR_RESET}"
 }
+# Wrap text in green color
 function __color_green()
 {
  local MSG="$1"
  echo -e "${CLR_GREEN}${MSG}${CLR_RESET}"
 }
+# Wrap text in blue color
 function __color_blue()
 {
  local MSG="$1"
@@ -48,36 +52,43 @@ function __color_blue()
 #  │ Helpers                                                  │
 #  ╰──────────────────────────────────────────────────────────╯

+# Print blue arrow marker
 function __log_marker()
 {
  echo -e "${CLR_BLUE}➜${CLR_RESET}"
 }

+# Print green checkmark marker
 function __log_marker_ok()
 {
  echo -e "${CLR_GREEN}✔${CLR_RESET}"
 }

+# Print blue checkmark marker
 function __log_marker_ok_blue()
 {
  echo -e "${CLR_BLUE}✔${CLR_RESET}"
 }

+# Print yellow warning marker
 function __log_marker_warn()
 {
  echo -e "${CLR_YELLOW}⁕${CLR_RESET}"
 }

+# Print yellow question marker
 function __log_marker_question()
 {
  echo -e "${CLR_YELLOW}?${CLR_RESET}"
 }

+# Print red error marker
 function __log_marker_err()
 {
  echo -e "${CLR_RED}⛌${CLR_RESET}"
 }

+# Print indentation spacing
 function __log_indent()
 {
  echo "    "
@@ -87,71 +98,85 @@ function __log_indent()
 #  │ Log functions                                            │
 #  ╰──────────────────────────────────────────────────────────╯

+# Print a message with arrow marker
 function msg()
 {
  echo -e "$(__log_marker) $1"
 }

+# Print a celebration message
 function msg_yay()
 {
  echo -e "🎉 $1"
 }

+# Print a celebration message with checkmark
 function msg_yay_done()
 {
  echo -e "🎉 $1 ...$(__log_marker_ok)"
 }

+# Print a message with completion checkmark
 function msg_done()
 {
  echo -e "$(__log_marker) $1 ...$(__log_marker_ok)"
 }

+# Print a completion checkmark suffix
 function msg_done_suffix()
 {
  echo -e "$(__log_marker) ...$(__log_marker_ok)"
 }

+# Print a prompt-style message
 function msg_prompt()
 {
  echo -e "$(__log_marker_question) $1"
 }

+# Print a prompt message with checkmark
 function msg_prompt_done()
 {
  echo -e "$(__log_marker_question) $1 ...$(__log_marker_ok)"
 }

+# Print an indented message
 function msg_nested()
 {
  echo -e "$(__log_indent)$(__log_marker) $1"
 }

+# Print an indented message with checkmark
 function msg_nested_done()
 {
  echo -e "$(__log_indent)$(__log_marker) $1 ...$(__log_marker_ok)"
 }

+# Print a running-task message in green
 function msg_run()
 {
  echo -e "${CLR_GREEN}➜ $1${CLR_RESET} $2"
 }

+# Print a running-task message with checkmark
 function msg_run_done()
 {
  echo -e "${CLR_GREEN}➜ $1${CLR_RESET} $2 ...$(__log_marker_ok)"
 }

+# Print an ok/success message
 function msg_ok()
 {
  echo -e "$(__log_marker_ok) $1"
 }

+# Print a warning message
 function msg_warn()
 {
  echo -e "$(__log_marker_warn) $1"
 }

+# Print an error message
 function msg_err()
 {
  echo -e "$(__log_marker_err) $1"
@@ -174,6 +199,7 @@ ask()
 # If this is being sourced, no need to run the next steps.
 [ "$sourced" = 1 ] && return

+# Run visual tests for all message types
 function __tests()
 {
  msg "[ msg ]"
@@ -192,6 +218,7 @@ function __tests()
  msg_yay_done "[ yay_done ]"
 }

+# Show usage information and examples
 function usage()
 {
  echo "usage: msgr [type] [message] [optional second message]"
--- a/local/bin/php-switcher
+++ b/local/bin/php-switcher
@@ -19,7 +19,7 @@ set -euo pipefail # Add error handling
 LATEST_VERSION_FORMULA="php"    # The formula name for latest PHP version
 PHP_VERSION_FILE=".php-version" # File name to look for when auto-switching

-# Switch brew php version
+# Verify that Homebrew is installed
 function check_dependencies()
 {
  if ! command -v brew > /dev/null 2>&1; then
@@ -28,6 +28,7 @@ function check_dependencies()
  fi
 }

+# Display help message and usage examples
 function usage()
 {
  echo "Brew PHP Switcher - Switch between PHP versions installed via Homebrew"
@@ -53,6 +54,7 @@ function usage()
  exit 0
 }

+# List all PHP versions installed via Homebrew
 function list_php_versions()
 {
  # Check Homebrew's installation path for PHP versions
@@ -185,6 +187,7 @@ function list_php_versions()
  done
 }

+# Convert a version number to a Homebrew formula name
 function get_php_formula_for_version()
 {
  local version="$1"
@@ -199,6 +202,7 @@ function get_php_formula_for_version()
  echo "php@$version"
 }

+# Check if a Homebrew formula is installed
 function check_formula_installed()
 {
  local formula="$1"
@@ -216,6 +220,7 @@ function check_formula_installed()
  return 1
 }

+# Unlink the currently active PHP version
 function unlink_current_php()
 {
  local current_formula=""
@@ -241,6 +246,7 @@ function unlink_current_php()
  fi
 }

+# Link a specific PHP formula as the active version
 function link_php_version()
 {
  local formula="$1"
@@ -265,6 +271,7 @@ function link_php_version()
  fi
 }

+# Display the currently active PHP version
 function get_current_version()
 {
  if ! command -v php > /dev/null 2>&1; then
@@ -300,6 +307,7 @@ function get_current_version()
  fi
 }

+# Validate PHP version format (x.y or latest)
 function validate_version()
 {
  local version="$1"
@@ -312,6 +320,7 @@ function validate_version()
  fi
 }

+# Search for .php-version file in directory hierarchy
 function find_php_version_file()
 {
  local dir="$PWD"
@@ -334,6 +343,7 @@ function find_php_version_file()
  return 1
 }

+# Auto-switch PHP based on .php-version file
 function auto_switch_php_version()
 {
  local version_file
@@ -360,6 +370,7 @@ function auto_switch_php_version()
  switch_php_version "$version"
 }

+# Switch to a specific PHP version
 function switch_php_version()
 {
  local version="$1"
@@ -398,6 +409,7 @@ function switch_php_version()
  echo "PHP executable: $(command -v php)"
 }

+# Parse arguments and dispatch to appropriate action
 function main()
 {
  local version=""
--- a/local/bin/pushover
+++ b/local/bin/pushover
@@ -5,6 +5,7 @@
 #
 # Modified by Ismo Vuorinen <https://github.com/ivuorinen> 2023

+# Display usage information for pushover
 __pushover_usage()
 {
  printf "pushover <options> <message>\n"
@@ -23,6 +24,7 @@ __pushover_usage()
  return 1
 }

+# Format an optional curl form field
 __pushover_opt_field()
 {
  field=$1
@@ -33,6 +35,7 @@ __pushover_opt_field()
  fi
 }

+# Send a pushover notification via curl
 __pushover_send_message()
 {
  device="${1:-}"
--- a/local/bin/x-codeql
+++ b/local/bin/x-codeql
@@ -10,6 +10,7 @@ VERSION="1.0.0"
 LANG_MAP="c:.c,.h|cpp:.cpp,.cc,.cxx,.hpp,.hxx|csharp:.cs|go:.go|java:.java|
 javascript:.js,.jsx,.mjs,.ts,.tsx|python:.py|ruby:.rb|swift:.swift"

+# Display usage information and options
 usage()
 {
  cat << EOF
@@ -24,22 +25,26 @@ EOF
  exit "${1:-0}"
 }

+# Log a timestamped message to stderr
 log()
 {
  printf '[%s] %s\n' "$(date '+%H:%M:%S')" "$*" >&2
 }
+# Log an error message and exit
 err()
 {
  log "ERROR: $*"
  exit 1
 }

+# Verify codeql binary is available in PATH
 check_codeql()
 {
  command -v codeql > /dev/null 2>&1 || err "codeql binary not found in PATH"
  log "Found codeql: $(codeql version --format=terse)"
 }

+# Get or create the CodeQL cache directory
 get_cache_dir()
 {
  cache="${XDG_CACHE_HOME:-$HOME/.cache}/codeql"
@@ -47,6 +52,7 @@ get_cache_dir()
  printf '%s' "$cache"
 }

+# Detect supported programming languages in source path
 detect_languages()
 {
  src_path="$1"
@@ -85,6 +91,7 @@ detect_languages()
  printf '%s' "$detected" | tr ' ' '\n' | sort -u | tr '\n' ' ' | sed 's/ $//'
 }

+# Create a CodeQL database for a language
 create_database()
 {
  lang="$1"
@@ -98,6 +105,7 @@ create_database()
    --overwrite
 }

+# Display analysis result statistics from SARIF file
 show_results_stats()
 {
  sarif_file="$1"
@@ -126,6 +134,7 @@ show_results_stats()
  return 0
 }

+# Run CodeQL analysis for a single language
 analyze_language()
 {
  lang="$1"
@@ -172,6 +181,7 @@ analyze_language()
  rm -rf "$db_path"
 }

+# Parse arguments and run CodeQL analysis pipeline
 main()
 {
  src_path="."
--- a/local/bin/x-compare-versions.py
+++ b/local/bin/x-compare-versions.py
@@ -24,7 +24,7 @@ str_to_operator = {
 def vercmp(expr):
    """Version Comparison function."""
    words = expr.split()
-    comparisons = [words[i: i + 3] for i in range(0, len(words) - 2, 2)]
+    comparisons = [words[i : i + 3] for i in range(0, len(words) - 2, 2)]
    for left, op_str, right in comparisons:
        compare_op = str_to_operator[op_str]
        if not compare_op(version.parse(left), version.parse(right)):
@@ -63,7 +63,7 @@ def test():
    except KeyError:
        pass
    else:
-        assert False, "invalid operator did not raise"
+        raise AssertionError("invalid operator did not raise")


 if __name__ == "__main__":
--- a/local/bin/x-env-list
+++ b/local/bin/x-env-list
@@ -190,6 +190,7 @@ get_custom_group()
  return 1
 }

+# Check if a key matches the skipped keys list
 is_skipped()
 {
  local key=$1
--- a/local/bin/x-git-largest-files.py
+++ b/local/bin/x-git-largest-files.py
@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8 -*-

 # Python script to find the largest files in a git repository.
 # The general method is based on the script in this blog post:
@@ -32,60 +31,60 @@

 # vim:tw=120:ts=4:ft=python:norl:

-from subprocess import check_output, Popen, PIPE
 import argparse
+import glob
 import signal
 import sys
+from subprocess import PIPE, Popen, check_output  # nosec B404

 sortByOnDiskSize = False

-class Blob(object):
-  sha1 = ''
-  size = 0
-  packed_size = 0
-  path = ''

-  def __init__(self, line):
-    cols = line.split()
-    self.sha1, self.size, self.packed_size = cols[0], int(cols[2]), int(cols[3])
+class Blob:
+    sha1 = ""
+    size = 0
+    packed_size = 0
+    path = ""

-  def __repr__(self):
-    return '{} - {} - {} - {}'.format(
-      self.sha1, self.size, self.packed_size, self.path)
+    def __init__(self, line):
+        cols = line.split()
+        self.sha1, self.size, self.packed_size = cols[0], int(cols[2]), int(cols[3])

-  def __lt__(self, other):
-    if (sortByOnDiskSize):
-      return self.size < other.size
-    else:
-      return self.packed_size < other.packed_size
+    def __repr__(self):
+        return f"{self.sha1} - {self.size} - {self.packed_size} - {self.path}"

-  def csv_line(self):
-    return "{},{},{},{}".format(
-      self.size/1024, self.packed_size/1024, self.sha1, self.path)
+    def __lt__(self, other):
+        if sortByOnDiskSize:
+            return self.size < other.size
+        else:
+            return self.packed_size < other.packed_size
+
+    def csv_line(self):
+        return f"{self.size / 1024},{self.packed_size / 1024},{self.sha1},{self.path}"


 def main():
-  global sortByOnDiskSize
+    global sortByOnDiskSize

-  signal.signal(signal.SIGINT, signal_handler)
+    signal.signal(signal.SIGINT, signal_handler)

-  args = parse_arguments()
-  sortByOnDiskSize = args.sortByOnDiskSize
-  size_limit = 1024*args.filesExceeding
+    args = parse_arguments()
+    sortByOnDiskSize = args.sortByOnDiskSize
+    size_limit = 1024 * args.filesExceeding

-  if args.filesExceeding > 0:
-    print("Finding objects larger than {}kB…".format(args.filesExceeding))
-  else:
-    print("Finding the {} largest objects…".format(args.matchCount))
+    if args.filesExceeding > 0:
+        print(f"Finding objects larger than {args.filesExceeding}kB…")
+    else:
+        print(f"Finding the {args.matchCount} largest objects…")

-  blobs = get_top_blobs(args.matchCount, size_limit)
+    blobs = get_top_blobs(args.matchCount, size_limit)

-  populate_blob_paths(blobs)
-  print_out_blobs(blobs)
+    populate_blob_paths(blobs)
+    print_out_blobs(blobs)


 def get_top_blobs(count, size_limit):
-  """Get top blobs from git repository
+    """Get top blobs from git repository

    Args:
        count (int): How many items to return
@@ -93,110 +92,141 @@ def get_top_blobs(count, size_limit):

    Returns:
        dict: Dictionary of Blobs
-  """
-  sort_column = 4
+    """
+    sort_column = 4

-  if sortByOnDiskSize:
-    sort_column = 3
+    if sortByOnDiskSize:
+        sort_column = 3

-  verify_pack = "git verify-pack -v `git rev-parse --git-dir`/objects/pack/pack-*.idx | grep blob | sort -k{}nr".format(sort_column)  # noqa: E501
-  output = check_output(verify_pack, shell=True).decode('utf-8').strip().split("\n")[:-1]  # noqa: E501
+    git_dir = check_output(["git", "rev-parse", "--git-dir"]).decode("utf-8").strip()  # nosec B603 # nosemgrep
+    idx_files = glob.glob(f"{git_dir}/objects/pack/pack-*.idx")
+    verify_pack = Popen(  # nosec B603
+        ["git", "verify-pack", "-v", *idx_files],
+        stdout=PIPE,
+        stderr=PIPE,
+    )
+    grep_blob = Popen(["grep", "blob"], stdin=verify_pack.stdout, stdout=PIPE, stderr=PIPE)  # nosec B603
+    if verify_pack.stdout:
+        verify_pack.stdout.close()
+    sort_cmd = Popen(  # nosec B603
+        ["sort", f"-k{sort_column}nr"],
+        stdin=grep_blob.stdout,
+        stdout=PIPE,
+        stderr=PIPE,
+    )
+    if grep_blob.stdout:
+        grep_blob.stdout.close()
+    output = [line for line in sort_cmd.communicate()[0].decode("utf-8").strip().split("\n") if line]

-  blobs = dict()
-  # use __lt__ to do the appropriate comparison
-  compare_blob = Blob("a b {} {} c".format(size_limit, size_limit))
-  for obj_line in output:
-    blob = Blob(obj_line)
+    blobs = {}
+    # use __lt__ to do the appropriate comparison
+    compare_blob = Blob(f"a b {size_limit} {size_limit} c")
+    for obj_line in output:
+        blob = Blob(obj_line)

-    if size_limit > 0:
-      if compare_blob < blob:
-        blobs[blob.sha1] = blob
-      else:
-        break
-    else:
-      blobs[blob.sha1] = blob
+        if size_limit > 0:
+            if compare_blob < blob:
+                blobs[blob.sha1] = blob
+            else:
+                break
+        else:
+            blobs[blob.sha1] = blob

-      if len(blobs) == count:
-        break
+            if len(blobs) == count:
+                break

-  return blobs
+    return blobs


 def populate_blob_paths(blobs):
-  """Populate blob paths that only have a path
+    """Populate blob paths that only have a path

-  Args:
-    blobs (Blob, dict): Dictionary of Blobs
-  """
-  if len(blobs):
-    print("Finding object paths…")
+    Args:
+      blobs (Blob, dict): Dictionary of Blobs
+    """
+    if len(blobs):
+        print("Finding object paths…")

-    # Only include revs which have a path. Other revs aren't blobs.
-    rev_list = "git rev-list --all --objects | awk '$2 {print}'"
-    all_object_lines = check_output(rev_list, shell=True).decode('utf-8').strip().split("\n")[:-1]  # noqa: E501
-    outstanding_keys = list(blobs.keys())
+        # Only include revs which have a path. Other revs aren't blobs.
+        rev_list = Popen(["git", "rev-list", "--all", "--objects"], stdout=PIPE, stderr=PIPE)  # nosec B603
+        awk_filter = Popen(["awk", "$2 {print}"], stdin=rev_list.stdout, stdout=PIPE, stderr=PIPE)  # nosec B603
+        if rev_list.stdout:
+            rev_list.stdout.close()
+        all_object_lines = [line for line in awk_filter.communicate()[0].decode("utf-8").strip().split("\n") if line]
+        outstanding_keys = list(blobs.keys())

-    for line in all_object_lines:
-      cols = line.split()
-      sha1, path = cols[0], " ".join(cols[1:])
+        for line in all_object_lines:
+            cols = line.split()
+            sha1, path = cols[0], " ".join(cols[1:])

-      if (sha1 in outstanding_keys):
-        outstanding_keys.remove(sha1)
-        blobs[sha1].path = path
+            if sha1 in outstanding_keys:
+                outstanding_keys.remove(sha1)
+                blobs[sha1].path = path

-        # short-circuit the search if we're done
-        if not len(outstanding_keys):
-          break
+                # short-circuit the search if we're done
+                if not len(outstanding_keys):
+                    break


 def print_out_blobs(blobs):
-  if len(blobs):
-    csv_lines = ["size,pack,hash,path"]
+    if len(blobs):
+        csv_lines = ["size,pack,hash,path"]

-    for blob in sorted(blobs.values(), reverse=True):
-      csv_lines.append(blob.csv_line())
+        for blob in sorted(blobs.values(), reverse=True):
+            csv_lines.append(blob.csv_line())

-    command = ["column", "-t", "-s", ","]
-    p = Popen(command, stdin=PIPE, stdout=PIPE, stderr=PIPE)
+        command = ["column", "-t", "-s", ","]
+        p = Popen(command, stdin=PIPE, stdout=PIPE, stderr=PIPE)

-    # Encode the input as bytes
-    input_data = ("\n".join(csv_lines) + "\n").encode()
+        # Encode the input as bytes
+        input_data = ("\n".join(csv_lines) + "\n").encode()

-    stdout, _ = p.communicate(input_data)
+        stdout, _ = p.communicate(input_data)

-    print("\nAll sizes in kB. The pack column is the compressed size of the object inside the pack file.\n")  # noqa: E501
+        print("\nAll sizes in kB. The pack column is the compressed size of the object inside the pack file.\n")

-    print(stdout.decode("utf-8").rstrip('\n'))
-  else:
-    print("No files found which match those criteria.")
+        print(stdout.decode("utf-8").rstrip("\n"))
+    else:
+        print("No files found which match those criteria.")


 def parse_arguments():
-  parser = argparse.ArgumentParser(
-    description='List the largest files in a git repository'
-  )
-  parser.add_argument(
-    '-c', '--match-count', dest='matchCount', type=int, default=10,
-    help='Files to return. Default is 10. Ignored if --files-exceeding is used.'
-  )
-  parser.add_argument(
-    '--files-exceeding', dest='filesExceeding', type=int, default=0,
-    help='The cutoff amount, in KB. Files with a pack size (or physical size, with -p) larger than this will be printed.' # noqa: E501
-  )
-  parser.add_argument(
-    '-p', '--physical-sort', dest='sortByOnDiskSize',
-    action='store_true', default=False,
-    help='Sort by the on-disk size. Default is to sort by the pack size.'
-  )
+    parser = argparse.ArgumentParser(description="List the largest files in a git repository")
+    parser.add_argument(
+        "-c",
+        "--match-count",
+        dest="matchCount",
+        type=int,
+        default=10,
+        help="Files to return. Default is 10. Ignored if --files-exceeding is used.",
+    )
+    parser.add_argument(
+        "--files-exceeding",
+        dest="filesExceeding",
+        type=int,
+        default=0,
+        help=(
+            "The cutoff amount, in KB. Files with a pack size"
+            " (or physical size, with -p) larger than this will be printed."
+        ),
+    )
+    parser.add_argument(
+        "-p",
+        "--physical-sort",
+        dest="sortByOnDiskSize",
+        action="store_true",
+        default=False,
+        help="Sort by the on-disk size. Default is to sort by the pack size.",
+    )

-  return parser.parse_args()
+    return parser.parse_args()


-def signal_handler(signal, frame):
-    print('Caught Ctrl-C. Exiting.')
+def signal_handler(_signal, _frame):
+    print("Caught Ctrl-C. Exiting.")
    sys.exit(0)


 # Default function is main()
-if __name__ == '__main__':
-  main()
+if __name__ == "__main__":
+    main()
--- a/local/bin/x-multi-ping
+++ b/local/bin/x-multi-ping
@@ -41,6 +41,7 @@ LOOP=0
 SLEEP=1
 TIMEOUT=5

+# Display usage information and options
 usage()
 {
  echo "Usage: $0 [--loop|--forever] [--sleep=N] hostname1 hostname2 ..."
--- a/local/bin/x-pr-comments
+++ b/local/bin/x-pr-comments
@@ -39,16 +39,19 @@ log_error()
 {
  echo -e "${RED}ERROR:${NC} $1" >&2
 }
+# Log a warning message
 log_warn()
 {
  echo -e "${YELLOW}WARN:${NC} $1" >&2
 }
+# Log an informational message
 log_info()
 {
  if [[ "${INFO:-0}" == "1" ]]; then
    echo -e "${GREEN}INFO:${NC} $1" >&2
  fi
 }
+# Log a debug message
 log_debug()
 {
  if [[ "${DEBUG:-0}" == "1" ]]; then
--- a/local/bin/x-sonarcloud
+++ b/local/bin/x-sonarcloud
@@ -49,16 +49,19 @@ log_error()
 {
  echo -e "${RED}ERROR:${NC} $1" >&2
 }
+# Log a warning message
 log_warn()
 {
  echo -e "${YELLOW}WARN:${NC} $1" >&2
 }
+# Log an informational message
 log_info()
 {
  if [[ "${INFO:-0}" == "1" ]]; then
    echo -e "${GREEN}INFO:${NC} $1" >&2
  fi
 }
+# Log a debug message
 log_debug()
 {
  if [[ "${DEBUG:-0}" == "1" ]]; then
@@ -467,24 +470,24 @@ EOF
 ## Next Steps for LLM Analysis

 1. **Validate against current code:**
-   - Check if mentioned files and lines still match the reported issues
-   - Verify issues are not already fixed in the current branch
-   - Identify false positives and explain why they are false positives
+  - Check if mentioned files and lines still match the reported issues
+  - Verify issues are not already fixed in the current branch
+  - Identify false positives and explain why they are false positives

 2. **Prioritize fixes:**
-   - Address BLOCKER and CRITICAL severity issues first
-   - Group fixes by file to minimize context switching
-   - Consider effort estimates when planning the fix order
+  - Address BLOCKER and CRITICAL severity issues first
+  - Group fixes by file to minimize context switching
+  - Consider effort estimates when planning the fix order

 3. **Group by file for implementation:**
-   - Batch changes to the same file together
-   - Consider dependencies between fixes
-   - Plan atomic commits per logical change group
+  - Batch changes to the same file together
+  - Consider dependencies between fixes
+  - Plan atomic commits per logical change group

 4. **Track progress:**
-   - Use todo lists and memory tools to track which issues are addressed
-   - Mark false positives with clear reasoning
-   - Verify fixes do not introduce new issues
+  - Use todo lists and memory tools to track which issues are addressed
+  - Mark false positives with clear reasoning
+  - Verify fixes do not introduce new issues
 EOF
 }

--- a/local/bin/x-ssh-audit
+++ b/local/bin/x-ssh-audit
@@ -154,6 +154,7 @@ get_state()
 # ERROR HANDLING AND CLEANUP
 # ============================================================================

+# Clean up temporary files and handle exit
 cleanup()
 {
  exit_code=$?
@@ -177,6 +178,7 @@ trap cleanup EXIT INT TERM
 # LOGGING FUNCTIONS
 # ============================================================================

+# Create audit directories and initialize log file
 setup_logging()
 {
  # Create all necessary directories
@@ -197,6 +199,7 @@ setup_logging()
  } >> "$LOG_FILE"
 }

+# Log a message with timestamp and severity level
 log_message()
 {
  level="$1"
@@ -225,6 +228,7 @@ log_message()
 # INPUT VALIDATION
 # ============================================================================

+# Validate hostname format for SSH connection
 validate_hostname()
 {
  hostname="$1"
@@ -244,6 +248,7 @@ validate_hostname()
  return 0
 }

+# Validate username format for SSH connection
 validate_username()
 {
  username="$1"
@@ -263,6 +268,7 @@ validate_username()
  return 0
 }

+# Parse input file into validated host entries
 parse_host_list()
 {
  input_file="$1"
@@ -309,6 +315,7 @@ parse_host_list()
 # SSH CONNECTION FUNCTIONS
 # ============================================================================

+# Execute SSH command with retry logic and key fallback
 ssh_with_retry()
 {
  host="$1"
@@ -373,6 +380,7 @@ ssh_with_retry()
  return 1
 }

+# Verify SSH connectivity to a host
 test_ssh_connectivity()
 {
  host="$1"
@@ -392,6 +400,7 @@ test_ssh_connectivity()
 # SSH SECURITY AUDIT FUNCTIONS
 # ============================================================================

+# Audit SSH daemon configuration on a remote host
 check_sshd_config()
 {
  host="$1"
@@ -451,6 +460,7 @@ check_sshd_config()
 # AUTOMATED UPDATES DETECTION
 # ============================================================================

+# Check if automated security updates are enabled
 check_automated_updates()
 {
  host="$1"
@@ -532,6 +542,7 @@ check_automated_updates()
 # PENDING REBOOT DETECTION
 # ============================================================================

+# Detect if a remote host requires a reboot
 check_pending_reboot()
 {
  host="$1"
@@ -602,6 +613,7 @@ check_pending_reboot()
 # REMEDIATION FUNCTIONS
 # ============================================================================

+# Create a timestamped backup of sshd_config
 backup_sshd_config()
 {
  host="$1"
@@ -616,6 +628,7 @@ backup_sshd_config()
    " "$ssh_key"
 }

+# Disable password authentication on a remote host
 disable_password_auth()
 {
  host="$1"
@@ -668,6 +681,7 @@ ClientAliveCountMax 2
 # REPORTING FUNCTIONS
 # ============================================================================

+# Generate CSV report from audit results
 generate_csv_report()
 {
  report_file="$1"
@@ -693,6 +707,7 @@ generate_csv_report()
  done < "$HOSTS_LIST_FILE"
 }

+# Display formatted audit summary to terminal
 display_summary()
 {
  printf '\n'
@@ -743,6 +758,7 @@ display_summary()
 # MAIN AUDIT FUNCTION
 # ============================================================================

+# Run all audit checks on a single host
 audit_host()
 {
  host_entry="$1"
@@ -788,6 +804,7 @@ audit_host()
 # MAIN EXECUTION
 # ============================================================================

+# Main entry point: parse args, run audits, generate report
 main()
 {
  input_file="${1:-}"
--- a/local/bin/x-term-colors
+++ b/local/bin/x-term-colors
@@ -9,11 +9,13 @@
 # <r> <g> <b> range from 0 to 255 inclusive.
 # The escape sequence ^[0m returns output to default

+# Set terminal background to an RGB color
 setBackgroundColor()
 {
  echo -en "\x1b[48;2;$1;$2;$3""m"
 }

+# Reset terminal output formatting
 resetOutput()
 {
  echo -en "\x1b[0m\n"
--- a/local/bin/x-thumbgen
+++ b/local/bin/x-thumbgen
@@ -28,6 +28,7 @@

 set -euo pipefail

+# Display usage information and options
 usage()
 {
  cat << EOF
@@ -52,6 +53,7 @@ THUMB_SUFFIX="${THUMB_SUFFIX:-_thumb}"
 # List of MIME types supported by ImageMagick (adjust as needed)
 ALLOWED_MIMETYPES=("image/jpeg" "image/png" "image/gif" "image/bmp" "image/tiff" "image/webp")

+# Verify ImageMagick is available
 check_magick_installed()
 {
  if ! command -v magick &> /dev/null; then
@@ -60,6 +62,7 @@ check_magick_installed()
  fi
 }

+# Verify mimetype command is available
 check_mimetype_installed()
 {
  if ! command -v mimetype &> /dev/null; then
@@ -165,6 +168,7 @@ generate_thumbnails()
  done < <(find "$source_dir" -type f -print0)
 }

+# Parse options, validate inputs, and generate thumbnails
 main()
 {
  parse_options "$@"
--- a/local/bin/x-when-down
+++ b/local/bin/x-when-down
@@ -26,6 +26,7 @@ if [ "$#" -lt 2 ]; then
  exit 1
 fi

+# Wait until host stops responding to ping
 wait_for_host_down()
 {
  local host=$1
@@ -37,6 +38,7 @@ wait_for_host_down()
  done
 }

+# Wait for host to go down then execute command
 main()
 {
  local host=$1
--- a/local/bin/x-when-up
+++ b/local/bin/x-when-up
@@ -30,6 +30,7 @@ if [ "$#" -lt 2 ]; then
  exit 1
 fi

+# Extract hostname from arguments, handling ssh shortcut
 get_host()
 {
  if [ "$1" = "ssh" ]; then
@@ -39,6 +40,7 @@ get_host()
  fi
 }

+# Wait until host responds to ping
 wait_for_host()
 {
  local host=$1
@@ -50,6 +52,7 @@ wait_for_host()
  done
 }

+# Wait for host to come online then execute command
 main()
 {
  local host