Parallelize status metric collection, enhance debug logging with a dedicated file and system info, update security audit for swap clearing, and remove orphaned cask cleaning.

lib/clean/apps.sh

@@ -79,15 +79,10 @@ clean_ds_store_tree() {
 # Clean data for uninstalled apps (caches/logs/states older than 60 days)
 # Protects system apps, major vendors, scans /Applications+running processes
 # Max 100 items/pattern, 2s du timeout. Env: ORPHAN_AGE_THRESHOLD, DRY_RUN
-clean_orphaned_app_data() {
+# Scan system for installed application bundle IDs
-    # Quick permission check - if we can't access Library folders, skip
+# Usage: scan_installed_apps "output_file"
-    if ! ls "$HOME/Library/Caches" > /dev/null 2>&1; then
+scan_installed_apps() {
-        echo -e "  ${YELLOW}${ICON_WARNING}${NC} Skipped: No permission to access Library folders"
+    local installed_bundles="$1"
-        return 0
-    fi
-
-    # Build list of installed/active apps
-    local installed_bundles=$(create_temp_file)
 
     # Scan all Applications directories
     local -a app_dirs=(
@@ -169,8 +164,8 @@ clean_orphaned_app_data() {
 
     (
         run_with_timeout 5 find ~/Library/LaunchAgents /Library/LaunchAgents \
-            -name "*.plist" -type f 2> /dev/null |
+             -name "*.plist" -type f 2> /dev/null |
-            xargs -I {} basename {} .plist > "$scan_tmp_dir/agents.txt" 2> /dev/null || true
+             xargs -I {} basename {} .plist > "$scan_tmp_dir/agents.txt" 2> /dev/null || true
     ) &
     pids+=($!)
 
@@ -193,56 +188,71 @@ clean_orphaned_app_data() {
 
     local app_count=$(wc -l < "$installed_bundles" 2> /dev/null | tr -d ' ')
     echo -e "  ${GREEN}${ICON_SUCCESS}${NC} Found $app_count active/installed apps"
+}
+
+# Check if bundle is orphaned
+# Usage: is_bundle_orphaned "bundle_id" "directory_path" "installed_bundles_file"
+is_bundle_orphaned() {
+    local bundle_id="$1"
+    local directory_path="$2"
+    local installed_bundles="$3"
+
+    # Skip system-critical and protected apps
+    if should_protect_data "$bundle_id"; then
+        return 1
+    fi
+
+    # Check if app exists in our scan
+    if grep -Fxq "$bundle_id" "$installed_bundles" 2> /dev/null; then
+        return 1
+    fi
+
+    # Check against centralized protected patterns (app_protection.sh)
+    if should_protect_data "$bundle_id"; then
+        return 1
+    fi
+
+
+    # Extra check for specific system bundles not covered by patterns
+    case "$bundle_id" in
+        loginwindow | dock | systempreferences | finder | safari)
+            return 1
+            ;;
+    esac
+
+    # Check file age - only clean if 60+ days inactive
+    # Use existing logic
+    if [[ -e "$directory_path" ]]; then
+        local last_modified_epoch=$(get_file_mtime "$directory_path")
+        local current_epoch=$(date +%s)
+        local days_since_modified=$(((current_epoch - last_modified_epoch) / 86400))
+
+        if [[ $days_since_modified -lt ${ORPHAN_AGE_THRESHOLD:-60} ]]; then
+            return 1
+        fi
+    fi
+
+    return 0
+}
+
+# Clean data for uninstalled apps (caches/logs/states older than 60 days)
+# Protects system apps, major vendors, scans /Applications+running processes
+# Max 100 items/pattern, 2s du timeout. Env: ORPHAN_AGE_THRESHOLD, DRY_RUN
+clean_orphaned_app_data() {
+    # Quick permission check - if we can't access Library folders, skip
+    if ! ls "$HOME/Library/Caches" > /dev/null 2>&1; then
+        echo -e "  ${YELLOW}${ICON_WARNING}${NC} Skipped: No permission to access Library folders"
+        return 0
+    fi
+
+    # Build list of installed/active apps
+    local installed_bundles=$(create_temp_file)
+    scan_installed_apps "$installed_bundles"
 
     # Track statistics
     local orphaned_count=0
     local total_orphaned_kb=0
 
-    # Check if bundle is orphaned - conservative approach
-    is_orphaned() {
-        local bundle_id="$1"
-        local directory_path="$2"
-
-        # Skip system-critical and protected apps
-        if should_protect_data "$bundle_id"; then
-            return 1
-        fi
-
-        # Check if app exists in our scan
-        if grep -Fxq "$bundle_id" "$installed_bundles" 2> /dev/null; then
-            return 1
-        fi
-
-        # Extra check for system bundles
-        case "$bundle_id" in
-            com.apple.* | loginwindow | dock | systempreferences | finder | safari)
-                return 1
-                ;;
-        esac
-
-        # Skip major vendors
-        case "$bundle_id" in
-            com.adobe.* | com.microsoft.* | com.google.* | org.mozilla.* | com.jetbrains.* | com.docker.*)
-                return 1
-                ;;
-        esac
-
-        # Check file age - only clean if 60+ days inactive
-        # Use modification time (mtime) instead of access time (atime)
-        # because macOS disables atime updates by default for performance
-        if [[ -e "$directory_path" ]]; then
-            local last_modified_epoch=$(get_file_mtime "$directory_path")
-            local current_epoch=$(date +%s)
-            local days_since_modified=$(((current_epoch - last_modified_epoch) / 86400))
-
-            if [[ $days_since_modified -lt ${ORPHAN_AGE_THRESHOLD:-60} ]]; then
-                return 1
-            fi
-        fi
-
-        return 0
-    }
-
     # Unified orphaned resource scanner (caches, logs, states, webkit, HTTP, cookies)
     MOLE_SPINNER_PREFIX="  " start_inline_spinner "Scanning orphaned app resources..."
 
@@ -300,7 +310,7 @@ clean_orphaned_app_data() {
                 bundle_id="${bundle_id%.savedState}"
                 bundle_id="${bundle_id%.binarycookies}"
 
-                if is_orphaned "$bundle_id" "$match"; then
+                if is_bundle_orphaned "$bundle_id" "$match" "$installed_bundles"; then
                     # Use timeout to prevent du from hanging on network mounts or problematic paths
                     local size_kb
                     size_kb=$(get_path_size_kb "$match")

lib/clean/brew.sh

@@ -38,26 +38,36 @@ clean_orphaned_casks() {
         rm -f "$cask_cache" 2> /dev/null || true
         true > "$cask_cache"
 
-        while IFS= read -r cask; do
+    while IFS= read -r cask; do
             # Get app path from cask info with timeout protection (expensive call, hence caching)
             local cask_info
             cask_info=$(run_with_timeout 10 brew info --cask "$cask" 2> /dev/null || true)
 
+            # SAFETY: Skip if cask contains non-App artifacts (Screen Savers, Plugins, etc.)
+            # This prevents accidental deletion of casks that don't primarily install to /Applications
+            if echo "$cask_info" | grep -qE '\((Screen Saver|Preference Pane|Audio Unit|VST|VST3|Component|QuickLook|Spotlight|Artifact)\)'; then
+                continue
+            fi
+
             # Extract app name from "AppName.app (App)" format in cask info output
             local app_name
             app_name=$(echo "$cask_info" | grep -E '\.app \(App\)' | head -1 | sed -E 's/^[[:space:]]*//' | sed -E 's/ \(App\).*//' || true)
 
-            # Skip if no app artifact (might be a utility package like fonts)
+            # Skip if no app artifact (might be a utility package like fonts or just drivers)
             [[ -z "$app_name" ]] && continue
 
             # Save to cache for future runs
             echo "$cask|$app_name" >> "$cask_cache"
 
-            # Check if app exists in /Applications
+            # Check if app exists into common locations
-            [[ ! -e "/Applications/$app_name" ]] && orphaned_casks+=("$cask")
+            # We must check both /Applications and ~/Applications
+            if [[ ! -e "/Applications/$app_name" ]] && [[ ! -e "$HOME/Applications/$app_name" ]]; then
+                 orphaned_casks+=("$cask")
+            fi
         done < <(brew list --cask 2> /dev/null || true)
     fi
 
+
     # Remove orphaned casks if found and sudo session is still valid
     if [[ ${#orphaned_casks[@]} -gt 0 ]]; then
         # Check if sudo session is still valid (without prompting)

lib/clean/system.sh

@@ -52,10 +52,7 @@ clean_deep_system() {
         fi
     fi
 
-    # Clean orphaned cask records (delegated to clean_brew module)
+
-    # DISABLED: This feature triggers password prompts and provides minimal benefit
-    # Users can manually run: brew list --cask && brew uninstall --cask <name>
-    # clean_orphaned_casks
 
     # Clean macOS Install Data (system upgrade leftovers)
     # Only remove if older than 30 days to ensure system stability

lib/clean/user.sh

@@ -193,11 +193,19 @@ clean_application_support_logs() {
         # Skip system and protected apps (case-insensitive)
         local app_name_lower
         app_name_lower=$(echo "$app_name" | tr '[:upper:]' '[:lower:]')
-        case "$app_name_lower" in
+        # Use centralized protection logic from app_protection.sh
-            com.apple.* | adobe* | jetbrains* | 1password | claude | *clashx* | *clash* | mihomo* | *surge* | iterm* | warp* | kitty* | alacritty* | wezterm* | ghostty*)
+        # Check against System Critical and Data Protected bundles
-                continue
+        local is_protected=false
-                ;;
+
-        esac
+        # Check if directory name matches any protected pattern
+        # We check both exact name and lowercase version against the patterns
+        if should_protect_data "$app_name"; then
+            is_protected=true
+        elif should_protect_data "$app_name_lower"; then
+            is_protected=true
+        fi
+
+        [[ "$is_protected" == "true" ]] && continue
 
         # Clean log directories - simple direct removal without deep scanning
         [[ -d "$app_dir/log" ]] && safe_clean "$app_dir/log"/* "App logs: $app_name"

lib/core/app_protection.sh

@@ -685,6 +685,107 @@ find_app_system_files() {
     if [[ ${#system_files[@]} -gt 0 ]]; then
         printf '%s\n' "${system_files[@]}"
     fi
+
+    # Find files from receipts (Deep Scan)
+    find_app_receipt_files "$bundle_id"
+}
+
+# Find files from installation receipts (Bom files)
+find_app_receipt_files() {
+    local bundle_id="$1"
+
+    # Skip if no bundle ID
+    [[ -z "$bundle_id" || "$bundle_id" == "unknown" ]] && return 0
+
+    local -a receipt_files=()
+    local -a bom_files=()
+
+    # Find receipts matching the bundle ID
+    # Usually in /var/db/receipts/
+    if [[ -d /private/var/db/receipts ]]; then
+        while IFS= read -r -d '' bom; do
+            bom_files+=("$bom")
+        done < <(find /private/var/db/receipts -name "${bundle_id}*.bom" -print0 2> /dev/null)
+    fi
+
+    for bom_file in "${bom_files[@]}"; do
+        [[ ! -f "$bom_file" ]] && continue
+
+        # Parse bom file
+        # lsbom -f: file paths only
+        # -s: suppress output (convert to text)
+        local bom_content
+        bom_content=$(lsbom -f -s "$bom_file" 2> /dev/null)
+
+        while IFS= read -r file_path; do
+            # Standardize path (remove leading dot)
+            local clean_path="${file_path#.}"
+
+            # Ensure it starts with /
+            if [[ "$clean_path" != /* ]]; then
+                clean_path="/$clean_path"
+            fi
+
+            # ------------------------------------------------------------------------
+            # SAFETY FILTER: Only allow specific removal paths
+            # ------------------------------------------------------------------------
+            local is_safe=false
+
+            # Whitelisted prefixes
+            case "$clean_path" in
+                /Applications/*) is_safe=true ;;
+                /Users/*)        is_safe=true ;;
+                /usr/local/*)    is_safe=true ;;
+                /opt/*)          is_safe=true ;;
+                /Library/*)
+                    # Filter sub-paths in /Library to avoid system damage
+                    # Allow safely: Application Support, Caches, Logs, Preferences
+                    case "$clean_path" in
+                        /Library/Application\ Support/*) is_safe=true ;;
+                        /Library/Caches/*)               is_safe=true ;;
+                        /Library/Logs/*)                 is_safe=true ;;
+                        /Library/Preferences/*)          is_safe=true ;;
+                        /Library/PrivilegedHelperTools/*) is_safe=true ;;
+                        /Library/LaunchAgents/*)         is_safe=true ;;
+                        /Library/LaunchDaemons/*)        is_safe=true ;;
+                        /Library/Internet\ Plug-Ins/*)   is_safe=true ;;
+                        /Library/Audio/Plug-Ins/*)       is_safe=true ;;
+                        /Library/Extensions/*)           is_safe=false ;; # Default unsafe
+                        *) is_safe=false ;;
+                    esac
+                    ;;
+            esac
+
+            # Hard blocks
+            case "$clean_path" in
+                /System/*|/usr/bin/*|/usr/lib/*|/bin/*|/sbin/*) is_safe=false ;;
+            esac
+
+            if [[ "$is_safe" == "true" && -e "$clean_path" ]]; then
+                # Only valid files
+                # Don't delete directories if they are non-empty parents?
+                # lsbom lists directories too.
+                # If we return a directory, `safe_remove` logic handles it.
+                # `uninstall.sh` uses `remove_file_list`.
+                # If `lsbom` lists `/Applications` (it shouldn't, only contents), we must be careful.
+                # `lsbom` usually lists `./Applications/MyApp.app`.
+                # If it lists `./Applications`, we must skip it.
+
+                # Extra check: path must be deep enough?
+                # If path is just "/Applications", skip.
+                if [[ "$clean_path" == "/Applications" || "$clean_path" == "/Library" || "$clean_path" == "/usr/local" ]]; then
+                   continue
+                fi
+
+                receipt_files+=("$clean_path")
+            fi
+
+        done <<< "$bom_content"
+    done
+
+    if [[ ${#receipt_files[@]} -gt 0 ]]; then
+        printf '%s\n' "${receipt_files[@]}"
+    fi
 }
 
 # Force quit an application

lib/core/common.sh

@@ -15,6 +15,7 @@ _MOLE_CORE_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 # Load core modules in dependency order
 source "$_MOLE_CORE_DIR/base.sh"
 source "$_MOLE_CORE_DIR/log.sh"
+
 source "$_MOLE_CORE_DIR/timeout.sh"
 source "$_MOLE_CORE_DIR/file_ops.sh"
 source "$_MOLE_CORE_DIR/ui.sh"

lib/core/log.sh

@@ -22,6 +22,7 @@ fi
 # ============================================================================
 
 readonly LOG_FILE="${HOME}/.config/mole/mole.log"
+readonly DEBUG_LOG_FILE="${HOME}/.config/mole/mole_debug_session.log"
 readonly LOG_MAX_SIZE_DEFAULT=1048576 # 1MB
 
 # Ensure log directory exists
@@ -53,28 +54,44 @@ rotate_log_once() {
 # Args: $1 - message
 log_info() {
     echo -e "${BLUE}$1${NC}"
-    echo "[$(date '+%Y-%m-%d %H:%M:%S')] INFO: $1" >> "$LOG_FILE" 2> /dev/null || true
+    local timestamp=$(date '+%Y-%m-%d %H:%M:%S')
+    echo "[$timestamp] INFO: $1" >> "$LOG_FILE" 2> /dev/null || true
+    if [[ "${MO_DEBUG:-}" == "1" ]]; then
+        echo "[$timestamp] INFO: $1" >> "$DEBUG_LOG_FILE" 2> /dev/null || true
+    fi
 }
 
 # Log success message
 # Args: $1 - message
 log_success() {
     echo -e "  ${GREEN}${ICON_SUCCESS}${NC} $1"
-    echo "[$(date '+%Y-%m-%d %H:%M:%S')] SUCCESS: $1" >> "$LOG_FILE" 2> /dev/null || true
+    local timestamp=$(date '+%Y-%m-%d %H:%M:%S')
+    echo "[$timestamp] SUCCESS: $1" >> "$LOG_FILE" 2> /dev/null || true
+    if [[ "${MO_DEBUG:-}" == "1" ]]; then
+        echo "[$timestamp] SUCCESS: $1" >> "$DEBUG_LOG_FILE" 2> /dev/null || true
+    fi
 }
 
 # Log warning message
 # Args: $1 - message
 log_warning() {
     echo -e "${YELLOW}$1${NC}"
-    echo "[$(date '+%Y-%m-%d %H:%M:%S')] WARNING: $1" >> "$LOG_FILE" 2> /dev/null || true
+    local timestamp=$(date '+%Y-%m-%d %H:%M:%S')
+    echo "[$timestamp] WARNING: $1" >> "$LOG_FILE" 2> /dev/null || true
+    if [[ "${MO_DEBUG:-}" == "1" ]]; then
+        echo "[$timestamp] WARNING: $1" >> "$DEBUG_LOG_FILE" 2> /dev/null || true
+    fi
 }
 
 # Log error message
 # Args: $1 - message
 log_error() {
     echo -e "${RED}${ICON_ERROR}${NC} $1" >&2
-    echo "[$(date '+%Y-%m-%d %H:%M:%S')] ERROR: $1" >> "$LOG_FILE" 2> /dev/null || true
+    local timestamp=$(date '+%Y-%m-%d %H:%M:%S')
+    echo "[$timestamp] ERROR: $1" >> "$LOG_FILE" 2> /dev/null || true
+    if [[ "${MO_DEBUG:-}" == "1" ]]; then
+        echo "[$timestamp] ERROR: $1" >> "$DEBUG_LOG_FILE" 2> /dev/null || true
+    fi
 }
 
 # Debug logging - only shown when MO_DEBUG=1
@@ -82,9 +99,46 @@ log_error() {
 debug_log() {
     if [[ "${MO_DEBUG:-}" == "1" ]]; then
         echo -e "${GRAY}[DEBUG]${NC} $*" >&2
+        echo "[$(date '+%Y-%m-%d %H:%M:%S')] DEBUG: $*" >> "$DEBUG_LOG_FILE" 2> /dev/null || true
     fi
 }
 
+# Log system information for debugging
+log_system_info() {
+    # Only allow once per session
+    [[ -n "${MOLE_SYS_INFO_LOGGED:-}" ]] && return 0
+    export MOLE_SYS_INFO_LOGGED=1
+
+    # Reset debug log file for this new session
+    : > "$DEBUG_LOG_FILE"
+
+    # Start block in debug log file
+    {
+        echo "----------------------------------------------------------------------"
+        echo "Mole Debug Session - $(date '+%Y-%m-%d %H:%M:%S')"
+        echo "----------------------------------------------------------------------"
+        echo "User: $USER"
+        echo "Hostname: $(hostname)"
+        echo "Architecture: $(uname -m)"
+        echo "Kernel: $(uname -r)"
+        if command -v sw_vers > /dev/null; then
+            echo "macOS: $(sw_vers -productVersion) ($(sw_vers -buildVersion))"
+        fi
+        echo "Shell: ${SHELL:-unknown} (${TERM:-unknown})"
+
+        # Check sudo status non-interactively
+        if sudo -n true 2>/dev/null; then
+            echo "Sudo Access: Active"
+        else
+            echo "Sudo Access: Required"
+        fi
+        echo "----------------------------------------------------------------------"
+    } >> "$DEBUG_LOG_FILE" 2> /dev/null || true
+
+    # Notification to stderr
+    echo -e "${GRAY}[DEBUG] Debug logging enabled. Session log: $DEBUG_LOG_FILE${NC}" >&2
+}
+
 # ============================================================================
 # Command Execution Wrappers
 # ============================================================================
@@ -100,9 +154,17 @@ run_silent() {
 # Returns: command exit code
 run_logged() {
     local cmd="$1"
-    if ! "$@" 2>&1 | tee -a "$LOG_FILE" > /dev/null; then
+    # Log to main file, and also to debug file if enabled
-        log_warning "Command failed: $cmd"
+    if [[ "${MO_DEBUG:-}" == "1" ]]; then
-        return 1
+        if ! "$@" 2>&1 | tee -a "$LOG_FILE" | tee -a "$DEBUG_LOG_FILE" > /dev/null; then
+            log_warning "Command failed: $cmd"
+            return 1
+        fi
+    else
+        if ! "$@" 2>&1 | tee -a "$LOG_FILE" > /dev/null; then
+            log_warning "Command failed: $cmd"
+            return 1
+        fi
     fi
     return 0
 }
@@ -143,6 +205,11 @@ print_summary_block() {
         echo -e "${detail}"
     done
     echo "$divider"
+
+    # If debug mode is on, remind user about the log file location
+    if [[ "${MO_DEBUG:-}" == "1" ]]; then
+        echo -e "${GRAY}Debug session log saved to:${NC} ${DEBUG_LOG_FILE}"
+    fi
 }
 
 # ============================================================================
@@ -151,3 +218,8 @@ print_summary_block() {
 
 # Perform log rotation check on module load
 rotate_log_once
+
+# If debug mode is enabled, log system info immediately
+if [[ "${MO_DEBUG:-}" == "1" ]]; then
+    log_system_info
+fi