Remove overlay filesystem functionality and add detection/removal capability

- Remove unused overlay filesystem configuration and references
- Remove overlayfs sections from all profile JSON files
- Remove OVERLAY_ENABLED/OVERLAY_PROTECT_CONFIGS from config
- Update documentation to focus on tmpfs optimization
- Add overlay detection and removal functionality for cleanup
- Add remove_overlays() function with safe unmounting
- Add overlay status reporting in final optimization summary
- Add test-overlay-detection.sh for testing detection logic
- Simplify codebase by removing complex unused features
- Focus on proven desktop optimizations (tmpfs, zram, kernel)

CHANGELOG.md

@@ -1,5 +1,26 @@
 # Changelog
 
+## [2025-09-23] - Overlay Filesystem Removal
+
+### Removed
+- **Overlay filesystem functionality**: Removed unused overlay filesystem features
+  - Removed `OVERLAY_ENABLED` and `OVERLAY_PROTECT_CONFIGS` from configuration
+  - Removed `overlayfs` sections from all profile JSON files
+  - Removed overlay references from documentation and scripts
+  - Added overlay detection and removal functionality for existing mounts
+
+### Added
+- **Overlay cleanup functionality**: Added ability to detect and remove overlay mounts
+  - `remove_overlays()` function to safely unmount overlay filesystems
+  - Automatic cleanup of overlay work/upper directories
+  - Removal of overlay entries from /etc/fstab
+  - User prompt when overlay mounts are detected
+
+### Rationale
+- Overlay filesystems are complex and rarely needed on desktop systems
+- Most users benefit more from tmpfs cache optimization than overlay complexity
+- Simplified codebase by removing unused/incomplete functionality
+
 ## [2025-09-23] - tmpfs Setup Fix
 
 ### Fixed

README.md

@@ -2,7 +2,7 @@
 
 🚀 **Intelligent system optimization toolkit for Linux desktop systems**
 
-This repository provides automated system tuning based on hardware detection, usage patterns, and best practices for tmpfs, overlay filesystems, and kernel parameter optimization.
+This repository provides automated system tuning based on hardware detection, usage patterns, and best practices for tmpfs and kernel parameter optimization.
 
 ## ✨ **NEW: One-Button Optimizer**
 
@@ -71,7 +71,7 @@ sudo ./tune-system.sh --auto
 
 ## 📊 Supported Optimizations
 
-- **Memory Management**: zram, tmpfs, overlay filesystems
+- **Memory Management**: zram, tmpfs optimization
 - **Kernel Tuning**: vm parameters, scheduler settings
 - **Cache Optimization**: Browser, IDE, package manager caches
 - **I/O Optimization**: Storage and network tuning

TMPFS_FIX_SUMMARY.md

@@ -1,7 +1,7 @@
-# tmpfs/Overlay Functionality Fix Summary
+# tmpfs Functionality Fix Summary
 
 ## 🐛 Issue Identified
-The `one-button-optimizer.sh` script was asking users if they wanted to create tmpfs/overlays, but when they chose "yes", nothing happened because the `setup_tmpfs` function was missing.
+The `one-button-optimizer.sh` script was asking users if they wanted to create tmpfs optimizations, but when they chose "yes", nothing happened because the `setup_tmpfs` function was missing.
 
 ## ✅ Problems Fixed
 
@@ -128,4 +128,4 @@ With the fix applied, users will see:
 - **Better system responsiveness** under load
 - **Automatic scaling** based on available hardware
 
-The tmpfs/overlay functionality now works as intended, providing intelligent, automatic optimization of cache directories with proper detection and sizing based on system capabilities.
+The tmpfs functionality now works as intended, providing intelligent, automatic optimization of cache directories with proper detection and sizing based on system capabilities.

configs/default.conf

@@ -24,8 +24,6 @@ CUSTOM_SWAPPINESS=""                # Leave empty for profile default
 CUSTOM_DIRTY_RATIO=""               # Leave empty for profile default
 
 # Advanced settings
-OVERLAY_ENABLED=false               # Enable overlay filesystems
-OVERLAY_PROTECT_CONFIGS=false       # Protect system configs with overlay
 SYSTEMD_SERVICE=true                # Install systemd service
 
 # Exclusions (space-separated paths)

demo-tmpfs-scan.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-# Demonstration script showing tmpfs/overlay detection and setup
+# Demonstration script showing tmpfs detection and setup
 # This script shows what would happen on a fresh system
 
 set -euo pipefail
@@ -27,7 +27,7 @@ error() {
     echo -e "${RED}[WOULD DO]${NC} $1"
 }
 
-echo "🔍 tmpfs/Overlay Detection and Setup Demonstration"
+echo "🔍 tmpfs Detection and Setup Demonstration"
 echo "=================================================="
 echo ""
 
@@ -117,7 +117,7 @@ simulate_fresh_system_scan() {
                 size=$(du -sh "$node_dir" 2>/dev/null | cut -f1)
                 project_path=$(dirname "$node_dir")
                 warn "    Found: $project_path ($size)"
-                error "    → Could create overlay mount for faster access"
+                error "    → Could cache in tmpfs for faster access"
             fi
         done
     fi

one-button-optimizer.sh

@@ -113,6 +113,31 @@ analyze_and_prompt() {
         echo "  🔍 Scanning system for cache directories..."
     fi
     
+    # === OVERLAY FILESYSTEM CHECK ===
+    echo "🗂️  Overlay Filesystem Analysis:"
+    local overlay_count=$(mount -t overlay | wc -l)
+    if [[ $overlay_count -gt 0 ]]; then
+        echo "  ⚠️  Found $overlay_count overlay mounts (deprecated for desktop use)"
+        echo "  📁 Current overlay mounts:"
+        mount -t overlay | head -3 | awk '{print "     " $3 " (overlay)"}' 
+        [[ $overlay_count -gt 3 ]] && echo "     ... and $((overlay_count - 3)) more"
+        echo ""
+        echo "  💡 Overlays are complex and rarely needed on desktop systems."
+        echo "  💡 Consider removing them unless specifically required."
+        needs_changes=true
+        read -p "  Would you like to remove overlay mounts? (y/N): " -n 1 -r
+        echo
+        if [[ $REPLY =~ ^[Yy]$ ]]; then
+            REMOVE_OVERLAYS=true
+        else
+            REMOVE_OVERLAYS=false
+        fi
+    else
+        echo "  ✅ No overlay mounts found (good - not needed for desktop)"
+        REMOVE_OVERLAYS=false
+    fi
+    echo ""
+    
     # Always analyze potential tmpfs candidates (even if already configured)
     local cache_analysis=""
     local total_cache_size=0
@@ -225,7 +250,7 @@ analyze_and_prompt() {
         if [[ -d /var/lib/flatpak ]]; then
             local flatpak_size=$(du -sm /var/lib/flatpak 2>/dev/null | cut -f1 || echo 0)
             if [[ $flatpak_size -gt 1000 ]]; then
-                additional_opportunities="${additional_opportunities}     Flatpak apps: ${flatpak_size}MB (consider overlayfs)\n"
+                additional_opportunities="${additional_opportunities}     Flatpak apps: ${flatpak_size}MB (consider tmpfs for .cache)\n"
             fi
         fi
         
@@ -535,6 +560,7 @@ analyze_and_prompt() {
     [[ $SETUP_TMPFS == true ]] && actions+=("tmpfs")
     [[ $SETUP_KERNEL == true ]] && actions+=("kernel")
     [[ $SETUP_SERVICE == true ]] && actions+=("service")
+    [[ $REMOVE_OVERLAYS == true ]] && actions+=("remove-overlays")
     
     if [[ ${#actions[@]} -gt 0 ]]; then
         echo "📋 Selected optimizations: ${actions[*]}"
@@ -551,7 +577,7 @@ analyze_and_prompt() {
     fi
     
     # Export variables for the optimization functions
-    export SETUP_ZRAM SETUP_TMPFS SETUP_KERNEL SETUP_SERVICE
+    export SETUP_ZRAM SETUP_TMPFS SETUP_KERNEL SETUP_SERVICE REMOVE_OVERLAYS
     export SYSTEM_RAM_GB=$ram_gb
 }
 
@@ -612,6 +638,58 @@ setup_zram() {
     success "zram reconfigured with ${zram_size}GB"
 }
 
+remove_overlays() {
+    if [[ $REMOVE_OVERLAYS != true ]]; then
+        return 0
+    fi
+    
+    log "Removing overlay filesystem mounts..."
+    
+    # Get list of overlay mounts
+    local overlay_mounts=$(mount -t overlay | awk '{print $3}')
+    
+    if [[ -z "$overlay_mounts" ]]; then
+        log "No overlay mounts found to remove"
+        return 0
+    fi
+    
+    # Unmount each overlay
+    echo "$overlay_mounts" | while read -r mount_point; do
+        if [[ -n "$mount_point" ]]; then
+            log "  Unmounting overlay: $mount_point"
+            if umount "$mount_point" 2>/dev/null; then
+                success "  Successfully unmounted: $mount_point"
+                
+                # Clean up overlay work directories if they exist in /tmp
+                local work_dir="/tmp/overlay-work$(basename "$mount_point")"
+                local upper_dir="/tmp/overlay-upper$(basename "$mount_point")"
+                
+                if [[ -d "$work_dir" ]]; then
+                    rm -rf "$work_dir"
+                    log "  Cleaned up work directory: $work_dir"
+                fi
+                
+                if [[ -d "$upper_dir" ]]; then
+                    rm -rf "$upper_dir"
+                    log "  Cleaned up upper directory: $upper_dir"
+                fi
+            else
+                warn "  Failed to unmount: $mount_point (may be in use)"
+            fi
+        fi
+    done
+    
+    # Remove any overlay entries from fstab
+    if [[ -f /etc/fstab ]] && grep -q "overlay" /etc/fstab; then
+        log "Removing overlay entries from /etc/fstab..."
+        cp /etc/fstab /etc/fstab.backup.$(date +%s)
+        grep -v "overlay" /etc/fstab > /etc/fstab.tmp && mv /etc/fstab.tmp /etc/fstab
+        success "Removed overlay entries from /etc/fstab"
+    fi
+    
+    success "Overlay filesystem cleanup completed"
+}
+
 setup_tmpfs() {
     if [[ $SETUP_TMPFS != true ]]; then
         return 0
@@ -934,6 +1012,14 @@ show_final_status() {
         echo "     📊 Total tmpfs allocated: ${total_mb}MB"
     fi
     
+    # overlay status
+    local overlay_count=$(mount -t overlay | wc -l)
+    if [[ $overlay_count -eq 0 ]]; then
+        echo "  🗂️  overlays: None (optimal for desktop systems)"
+    else
+        echo "  ⚠️  overlays: $overlay_count mounts found (consider removal)"
+    fi
+    
     # kernel with current values
     if [[ -f /etc/sysctl.d/99-system-optimization.conf ]]; then
         local swappiness=$(sysctl -n vm.swappiness 2>/dev/null)
@@ -986,6 +1072,7 @@ main() {
     analyze_and_prompt
     
     # Apply selected optimizations
+    remove_overlays
     setup_zram
     setup_tmpfs
     tune_kernel

profiles/desktop.json

@@ -58,10 +58,6 @@
       "net.core.netdev_max_backlog": 5000,
       "net.core.rmem_max": 16777216,
       "net.core.wmem_max": 16777216
-    },
-    "overlayfs": {
-      "enabled": false,
-      "protect_configs": false
     }
   },
   "sizing_rules": {

profiles/development.json

@@ -58,14 +58,6 @@
       "fs.file-max": 2097152,
       "fs.inotify.max_user_watches": 524288,
       "kernel.pid_max": 32768
-    },
-    "overlayfs": {
-      "enabled": true,
-      "protect_configs": true,
-      "overlay_paths": [
-        "/home/*/workspace",
-        "/opt/projects"
-      ]
     }
   },
   "development_specific": {

profiles/gaming.json

@@ -48,9 +48,6 @@
       "net.core.netdev_max_backlog": 10000,
       "net.core.rmem_max": 33554432,
       "net.core.wmem_max": 33554432
-    },
-    "overlayfs": {
-      "enabled": false
     }
   },
   "gaming_specific": {

test-overlay-detection.sh

@@ -0,0 +1,113 @@
+#!/bin/bash
+# Test script to verify overlay detection and removal functionality
+# This script creates a temporary overlay mount and tests detection
+
+set -euo pipefail
+
+# Colors
+RED='\033[0;31m'
+GREEN='\033[0;32m'
+YELLOW='\033[1;33m'
+BLUE='\033[0;34m'
+NC='\033[0m'
+
+log() {
+    echo -e "${BLUE}[TEST]${NC} $1"
+}
+
+success() {
+    echo -e "${GREEN}[SUCCESS]${NC} $1"
+}
+
+warn() {
+    echo -e "${YELLOW}[WARNING]${NC} $1"
+}
+
+error() {
+    echo -e "${RED}[ERROR]${NC} $1"
+}
+
+echo "🔍 Testing Overlay Detection Functionality"
+echo "=========================================="
+echo ""
+
+# Check if running as root (needed for mount operations)
+if [[ $EUID -eq 0 ]]; then
+    warn "Running as root - will test actual mount/unmount operations"
+    CAN_MOUNT=true
+else
+    log "Running as non-root - will test detection logic only"
+    CAN_MOUNT=false
+fi
+
+# Test 1: Check current overlay mounts
+log "Test 1: Checking for existing overlay mounts..."
+overlay_count=$(mount -t overlay 2>/dev/null | wc -l)
+if [[ $overlay_count -eq 0 ]]; then
+    success "No existing overlay mounts found (expected for desktop systems)"
+else
+    warn "Found $overlay_count existing overlay mounts:"
+    mount -t overlay | awk '{print "  " $3}'
+fi
+echo ""
+
+# Test 2: Test detection function (simulated)
+log "Test 2: Testing overlay detection logic..."
+cat << 'EOF'
+# This is what the detection code does:
+overlay_count=$(mount -t overlay | wc -l)
+if [[ $overlay_count -gt 0 ]]; then
+    echo "Found $overlay_count overlay mounts"
+    mount -t overlay | awk '{print "  " $3 " (overlay)"}'
+else
+    echo "No overlay mounts found"
+fi
+EOF
+
+echo ""
+log "Running detection logic:"
+if [[ $overlay_count -gt 0 ]]; then
+    echo "  ⚠️  Found $overlay_count overlay mounts (would suggest removal)"
+    mount -t overlay | head -3 | awk '{print "     " $3 " (overlay)"}' 
+else
+    echo "  ✅ No overlay mounts found (good - not needed for desktop)"
+fi
+echo ""
+
+# Test 3: Test temporary overlay creation (if root)
+if [[ $CAN_MOUNT == true ]]; then
+    log "Test 3: Creating temporary overlay for testing..."
+    
+    # Create temporary directories
+    mkdir -p /tmp/overlay-test/{lower,upper,work,merged}
+    echo "test content" > /tmp/overlay-test/lower/testfile.txt
+    
+    # Create overlay mount
+    if mount -t overlay overlay -o lowerdir=/tmp/overlay-test/lower,upperdir=/tmp/overlay-test/upper,workdir=/tmp/overlay-test/work /tmp/overlay-test/merged 2>/dev/null; then
+        success "Created test overlay mount at /tmp/overlay-test/merged"
+        
+        # Test detection again
+        new_overlay_count=$(mount -t overlay | wc -l)
+        log "Detection now shows: $new_overlay_count overlay mounts"
+        
+        # Clean up
+        log "Cleaning up test overlay..."
+        umount /tmp/overlay-test/merged 2>/dev/null || true
+        rm -rf /tmp/overlay-test
+        success "Test overlay cleaned up"
+    else
+        error "Failed to create test overlay (this is normal on some systems)"
+        rm -rf /tmp/overlay-test
+    fi
+else
+    log "Test 3: Skipped (requires root privileges)"
+fi
+
+echo ""
+success "Overlay detection test completed!"
+echo ""
+log "Summary:"
+echo "  • Overlay detection logic works correctly"
+echo "  • Current system has $overlay_count overlay mounts"
+echo "  • Desktop systems typically don't need overlay filesystems"
+echo "  • The optimizer will offer to remove any found overlays"

test-tmpfs-detection.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-# Test script to verify tmpfs/overlay detection functionality
+# Test script to verify tmpfs detection functionality
 # This script can be run without root to test the detection logic
 
 set -euo pipefail
@@ -22,7 +22,7 @@ warn() {
     echo -e "${YELLOW}[INFO]${NC} $1"
 }
 
-echo "🔍 Testing tmpfs/overlay Detection Functionality"
+echo "🔍 Testing tmpfs Detection Functionality"
 echo "=============================================="
 echo ""