add update.sh: OS detection + package list update

- New update.sh: detects Alpine, Arch, Debian/Ubuntu, RHEL/Fedora/CentOS,
  openSUSE, Void, Gentoo and updates the package index only (no upgrades)
- clean.sh fixes:
  - Fix ((cleaned_count++)) exiting under set -e on first successful rm
  - Stop recursively deleting /var/cache and /root/.cache wholesale
  - Add CACHE_RETENTION_DAYS (7d) — clean_directory now only deletes
    files older than retention period instead of wiping everything
  - Remove dangerous rm -rf fallback in clean_directory
  - Narrow CACHE_DIRS to /var/cache/apt instead of /var/cache
  - Fix /home/*/.cache pattern to only target pip/npm caches

clean.sh

@@ -20,8 +20,9 @@ readonly YELLOW='\033[1;33m'
 # Cleanup configuration
 readonly LOG_RETENTION_DAYS=30
 readonly JOURNAL_RETENTION_DAYS=7
+readonly CACHE_RETENTION_DAYS=7
 readonly TEMP_DIRS=("/tmp" "/var/tmp")
-readonly CACHE_DIRS=("/var/cache" "/root/.cache")
+readonly CACHE_DIRS=("/var/cache/apt" "/root/.cache")
 
 #==============================================================================
 # UTILITY FUNCTIONS
@@ -56,6 +57,7 @@ get_dir_size() {
 }
 
 # Safe directory cleanup with size reporting
+# Deletes files older than CACHE_RETENTION_DAYS instead of wiping everything
 clean_directory() {
     local dir="$1"
     local description="$2"
@@ -74,16 +76,26 @@ clean_directory() {
     
     log_step "$description (was $size_before)..."
     
-    # Use find with -delete for safer cleanup
-    if find "$dir" -mindepth 1 -delete 2>/dev/null; then
-        log_success "$description: freed $size_before"
-    else
-        # Fallback to rm if find fails
-        if rm -rf "$dir"/* 2>/dev/null; then
-            log_success "$description: freed $size_before"
+    # Use find to delete files older than retention period
+    # -type f -mtime +N: only files older than N days (not directories)
+    local deleted=false
+    if find "$dir" -type f -mtime +"${CACHE_RETENTION_DAYS:-7}" -delete 2>/dev/null; then
+        deleted=true
+    fi
+    
+    # Clean up empty directories left behind (but don't remove the dir itself)
+    find "$dir" -mindepth 1 -type d -empty -delete 2>/dev/null || true
+    
+    if $deleted; then
+        local size_after
+        size_after=$(get_dir_size "$dir")
+        if [[ "$size_after" == "$size_before" ]]; then
+            log_info "$description: nothing old enough to clean (retention: ${CACHE_RETENTION_DAYS:-7}d)"
         else
-            log_warning "$description: partial cleanup completed"
+            log_success "$description: freed (was $size_before, now $size_after)"
         fi
+    else
+        log_warning "$description: partial cleanup completed"
     fi
 }
 
@@ -269,13 +281,19 @@ cleanup_cache_dirs() {
         fi
     done
     
-    # Clean additional cache locations
+    # Clean safe cache locations only
+    # NOTE: We do NOT recursively delete /var/cache or /root/.cache as a whole,
+    # as that can break package managers and remove important data.
     local additional_caches=(
-        "/var/lib/apt/lists"
+        "/var/cache/apt/archives"
+        "/var/cache/apt/archives/partial"
         "/var/cache/debconf"
+        "/var/lib/apt/lists"
         "/root/.npm"
-        "/root/.pip"
-        "/home/*/.cache"
+        "/root/.cache/pip"
+        "/root/.cache/npm"
+        "/home/*/.cache/pip"
+        "/home/*/.cache/npm"
         "/home/*/.npm"
         "/home/*/.pip"
     )
@@ -300,12 +318,16 @@ cleanup_logs() {
         
         # Find and remove old log files
         while IFS= read -r -d '' logfile; do
-            rm -f "$logfile" 2>/dev/null && ((cleaned_count++))
+            if rm -f "$logfile" 2>/dev/null; then
+                ((++cleaned_count)) || true
+            fi
         done < <(find /var/log -type f -name "*.log" -mtime +"$LOG_RETENTION_DAYS" -print0 2>/dev/null || true)
         
         # Clean compressed logs
         while IFS= read -r -d '' logfile; do
-            rm -f "$logfile" 2>/dev/null && ((cleaned_count++))
+            if rm -f "$logfile" 2>/dev/null; then
+                ((++cleaned_count)) || true
+            fi
         done < <(find /var/log -type f \( -name "*.log.gz" -o -name "*.log.bz2" -o -name "*.log.xz" \) -mtime +"$LOG_RETENTION_DAYS" -print0 2>/dev/null || true)
         
         if [[ $cleaned_count -gt 0 ]]; then