Fix search problems and best practices

bin/clean.sh

@@ -456,7 +456,10 @@ safe_clean() {
 }
 
 start_cleanup() {
-    clear
+    if [[ -t 1 ]]; then
+        # Avoid relying on TERM since CI often runs without it
+        printf '\033[2J\033[H'
+    fi
     printf '\n'
     echo -e "${PURPLE_BOLD}Clean Your Mac${NC}"
     echo ""

bin/uninstall.sh

@@ -73,11 +73,12 @@ scan_applications() {
     local cache_dir="$HOME/.cache/mole"
     local cache_file="$cache_dir/app_scan_cache"
     local cache_ttl=86400 # 24 hours
+    local force_rescan="${1:-false}"
 
     mkdir -p "$cache_dir" 2> /dev/null
 
     # Check if cache exists and is fresh
-    if [[ -f "$cache_file" ]]; then
+    if [[ $force_rescan == false && -f "$cache_file" ]]; then
         local cache_age=$(($(date +%s) - $(get_file_mtime "$cache_file")))
         [[ $cache_age -eq $(date +%s) ]] && cache_age=86401 # Handle missing file
         if [[ $cache_age -lt $cache_ttl ]]; then
@@ -405,11 +406,15 @@ trap cleanup EXIT INT TERM
 # Main function
 main() {
     # Parse args
+    local force_rescan=false
     for arg in "$@"; do
         case "$arg" in
             "--debug")
                 export MO_DEBUG=1
                 ;;
+            "--force-rescan")
+                force_rescan=true
+                ;;
         esac
     done
 
@@ -425,7 +430,7 @@ main() {
     # (scan_applications handles cache internally)
     local needs_scanning=true
     local cache_file="$HOME/.cache/mole/app_scan_cache"
-    if [[ -f "$cache_file" ]]; then
+    if [[ $force_rescan == false && -f "$cache_file" ]]; then
         local cache_age=$(($(date +%s) - $(get_file_mtime "$cache_file")))
         [[ $cache_age -eq $(date +%s) ]] && cache_age=86401 # Handle missing file
         [[ $cache_age -lt 86400 ]] && needs_scanning=false
@@ -444,7 +449,7 @@ main() {
 
     # Scan applications
     local apps_file=""
-    if ! apps_file=$(scan_applications); then
+    if ! apps_file=$(scan_applications "$force_rescan"); then
         if [[ "${MOLE_ALT_SCREEN_ACTIVE:-}" == "1" ]]; then
             printf "\033[2J\033[H" >&2
             leave_alt_screen

lib/core/common.sh

@@ -73,3 +73,93 @@ update_via_homebrew() {
     # Clear update cache
     rm -f "$HOME/.cache/mole/version_check" "$HOME/.cache/mole/update_message" 2> /dev/null || true
 }
+
+# Remove apps from Dock
+# Args: app paths to remove
+remove_apps_from_dock() {
+    if [[ $# -eq 0 ]]; then
+        return 0
+    fi
+
+    local plist="$HOME/Library/Preferences/com.apple.dock.plist"
+    [[ -f "$plist" ]] || return 0
+
+    if ! command -v python3 > /dev/null 2>&1; then
+        return 0
+    fi
+
+    # Execute Python helper to prune dock entries for the given app paths
+    python3 - "$@" << 'PY' 2>/dev/null || return 0
+import os
+import plistlib
+import subprocess
+import sys
+import urllib.parse
+
+plist_path = os.path.expanduser('~/Library/Preferences/com.apple.dock.plist')
+if not os.path.exists(plist_path):
+    sys.exit(0)
+
+def normalise(path):
+    if not path:
+        return ''
+    return os.path.normpath(os.path.realpath(path.rstrip('/')))
+
+targets = {normalise(arg) for arg in sys.argv[1:] if arg}
+targets = {t for t in targets if t}
+if not targets:
+    sys.exit(0)
+
+with open(plist_path, 'rb') as fh:
+    try:
+        data = plistlib.load(fh)
+    except Exception:
+        sys.exit(0)
+
+apps = data.get('persistent-apps')
+if not isinstance(apps, list):
+    sys.exit(0)
+
+changed = False
+filtered = []
+for item in apps:
+    try:
+        url = item['tile-data']['file-data']['_CFURLString']
+    except (KeyError, TypeError):
+        filtered.append(item)
+        continue
+
+    if not isinstance(url, str):
+        filtered.append(item)
+        continue
+
+    parsed = urllib.parse.urlparse(url)
+    path = urllib.parse.unquote(parsed.path or '')
+    if not path:
+        filtered.append(item)
+        continue
+
+    candidate = normalise(path)
+    if any(candidate == t or candidate.startswith(t + os.sep) for t in targets):
+        changed = True
+        continue
+
+    filtered.append(item)
+
+if not changed:
+    sys.exit(0)
+
+data['persistent-apps'] = filtered
+with open(plist_path, 'wb') as fh:
+    try:
+        plistlib.dump(data, fh, fmt=plistlib.FMT_BINARY)
+    except Exception:
+        plistlib.dump(data, fh)
+
+# Restart Dock to apply changes
+try:
+    subprocess.run(['killall', 'Dock'], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL, check=False)
+except Exception:
+    pass
+PY
+}

lib/core/ui.sh

@@ -49,6 +49,9 @@ read_key() {
     case "$key" in
         $'\n' | $'\r') echo "ENTER" ;;
         ' ') echo "SPACE" ;;
+        '/') echo "FILTER" ;;
+        'q' | 'Q') echo "QUIT" ;;
+        'R') echo "RETRY" ;;
         $'\x03') echo "QUIT" ;;
         $'\x7f' | $'\x08') echo "DELETE" ;;
         $'\x1b')

lib/manage/whitelist.sh

@@ -11,16 +11,25 @@ source "$_MOLE_MANAGE_DIR/../ui/menu_simple.sh"
 
 # Config file paths
 readonly WHITELIST_CONFIG_CLEAN="$HOME/.config/mole/whitelist"
-readonly WHITELIST_CONFIG_OPTIMIZE="$HOME/.config/mole/whitelist_checks"
+readonly WHITELIST_CONFIG_OPTIMIZE="$HOME/.config/mole/whitelist_optimize"
+readonly WHITELIST_CONFIG_OPTIMIZE_LEGACY="$HOME/.config/mole/whitelist_checks"
 
 # Default whitelist patterns defined in lib/core/common.sh:
 # - DEFAULT_WHITELIST_PATTERNS
 # - FINDER_METADATA_SENTINEL
 
-# Save whitelist patterns to config
+# Save whitelist patterns to config (defaults to "clean" for legacy callers)
 save_whitelist_patterns() {
-    local mode="$1"
-    shift
+    local mode="clean"
+    if [[ $# -gt 0 ]]; then
+        case "$1" in
+            clean | optimize)
+                mode="$1"
+                shift
+                ;;
+        esac
+    fi
+
     local -a patterns
     patterns=("$@")
     
@@ -170,13 +179,21 @@ load_whitelist() {
     local mode="${1:-clean}"
     local -a patterns=()
     local config_file
+    local legacy_file=""
 
     if [[ "$mode" == "optimize" ]]; then
         config_file="$WHITELIST_CONFIG_OPTIMIZE"
+        legacy_file="$WHITELIST_CONFIG_OPTIMIZE_LEGACY"
     else
         config_file="$WHITELIST_CONFIG_CLEAN"
     fi
 
+    local using_legacy="false"
+    if [[ ! -f "$config_file" && -n "$legacy_file" && -f "$legacy_file" ]]; then
+        config_file="$legacy_file"
+        using_legacy="true"
+    fi
+
     if [[ -f "$config_file" ]]; then
         while IFS= read -r line; do
             # shellcheck disable=SC2295
@@ -210,6 +227,11 @@ load_whitelist() {
             unique_patterns+=("$pattern")
         done
         CURRENT_WHITELIST_PATTERNS=("${unique_patterns[@]}")
+
+        # Migrate legacy optimize config to the new path automatically
+        if [[ "$mode" == "optimize" && "$using_legacy" == "true" && "$config_file" != "$WHITELIST_CONFIG_OPTIMIZE" ]]; then
+            save_whitelist_patterns "$mode" "${CURRENT_WHITELIST_PATTERNS[@]}"
+        fi
     else
         CURRENT_WHITELIST_PATTERNS=()
     fi

lib/ui/menu_paginated.sh

@@ -399,7 +399,7 @@ paginated_multi_select() {
                 for ((i = 0; i < items_per_page; i++)); do
                     printf "${clear_line}\n" >&2
                 done
-                printf "${clear_line}${GRAY}Type to filter  |  Delete  |  Enter  |  / Exit  |  ESC${NC}\n" >&2
+                printf "${clear_line}${GRAY}Type to filter  |  Delete  |  Enter Confirm  |  ESC Cancel${NC}\n" >&2
                 printf "${clear_line}" >&2
                 return
             else
@@ -480,9 +480,8 @@ paginated_multi_select() {
             local -a _segs_filter=(
                 "${GRAY}Filter: ${filter_status}${NC}"
                 "${GRAY}Delete${NC}"
-                "${GRAY}Enter${NC}"
-                "${GRAY}/ Exit${NC}"
-                "${GRAY}ESC${NC}"
+                "${GRAY}Enter Confirm${NC}"
+                "${GRAY}ESC Cancel${NC}"
             )
             _print_wrapped_controls "$sep" "${_segs_filter[@]}"
         else
@@ -668,15 +667,8 @@ paginated_multi_select() {
             CHAR:*)
                 if [[ "$filter_mode" == "true" ]]; then
                     local ch="${key#CHAR:}"
-                    # Special handling for /: exit filter mode
-                    if [[ "$ch" == "/" ]]; then
-                        filter_mode="false"
-                        unset MOLE_READ_KEY_FORCE_CHAR
-                        filter_query=""
-                        applied_query=""
-                        rebuild_view
                     # avoid accidental leading spaces
-                    elif [[ -n "$filter_query" || "$ch" != " " ]]; then
+                    if [[ -n "$filter_query" || "$ch" != " " ]]; then
                         filter_query+="$ch"
                     fi
                 fi

lib/uninstall/batch.sh

@@ -113,7 +113,6 @@ batch_uninstall_applications() {
     local -a sudo_apps=()
     local total_estimated_size=0
     local -a app_details=()
-    local -a dock_cleanup_paths=()
 
     # Analyze selected apps with progress indicator
     if [[ -t 1 ]]; then start_inline_spinner "Scanning files..."; fi
@@ -315,7 +314,6 @@ batch_uninstall_applications() {
             ((files_cleaned++))
             ((total_items++))
             success_items+=("$app_name")
-            dock_cleanup_paths+=("$app_path")
         else
             ((failed_count++))
             failed_items+=("$app_name:$reason")
@@ -406,8 +404,22 @@ batch_uninstall_applications() {
     print_summary_block "$summary_status" "Uninstall complete" "${summary_details[@]}"
     printf '\n'
 
-    if [[ ${#dock_cleanup_paths[@]} -gt 0 ]]; then
-        remove_apps_from_dock "${dock_cleanup_paths[@]}"
+    # Clean up Dock entries for uninstalled apps
+    if [[ $success_count -gt 0 ]]; then
+        local -a removed_paths=()
+        for detail in "${app_details[@]}"; do
+            IFS='|' read -r app_name app_path _ _ _ _ <<< "$detail"
+            # Check if this app was successfully removed
+            for success_name in "${success_items[@]}"; do
+                if [[ "$success_name" == "$app_name" ]]; then
+                    removed_paths+=("$app_path")
+                    break
+                fi
+            done
+        done
+        if [[ ${#removed_paths[@]} -gt 0 ]]; then
+            remove_apps_from_dock "${removed_paths[@]}" 2>/dev/null || true
+        fi
     fi
 
     # Clean up sudo keepalive if it was started