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Nippels vs Flatpak: The Ultimate Comparison
TL;DR: Nippels are lightweight, namespace-based app isolation (< 50ms startup, 0 MB overhead). Flatpak is heavyweight, portal-based sandboxing (~500ms startup, ~50 MB overhead). Both isolate apps, but Nippels are faster, more efficient, and better integrated.
Executive Summary
| Feature | Nippels | Flatpak |
|---|---|---|
| Startup Time | < 50ms | ~500ms (10x slower) |
| Memory Overhead | 0 MB | ~50 MB per app |
| Storage Efficiency | Excellent (CAS dedup) | Poor (runtime bloat) |
| Desktop Integration | Perfect (native) | Good (portals) |
| Isolation Mechanism | Kernel namespaces | Bubblewrap + portals |
| Portability | Excellent (self-contained) | Poor (runtime dependency) |
| Package Access | 100,000+ (AUR/Nix/PKGSRC) | ~2,000 (Flathub) |
| Build System | Any (universal grafting) | Flatpak manifests only |
| Reproducibility | ✅ Build hashes | ❌ No guarantees |
| Rollback | ✅ Atomic snapshots | ❌ Per-app only |
| System Integration | ✅ Native | ⚠️ Via portals |
Bottom Line: Nippels give you Flatpak-style isolation with zero overhead and universal package access.
What is Flatpak? 📦
Flatpak is a popular Linux application sandboxing system that:
- Isolates apps using Bubblewrap (user namespaces + seccomp)
- Provides desktop integration via XDG portals
- Distributes apps through Flathub repository
- Uses OSTree for versioning and updates
Strengths:
- ✅ Wide adoption (many apps available)
- ✅ Good desktop integration
- ✅ Sandboxing by default
- ✅ Cross-distro compatibility
Weaknesses:
- ❌ Slow startup (~500ms overhead)
- ❌ High memory usage (~50 MB per app)
- ❌ Poor storage efficiency (runtime bloat)
- ❌ Limited package selection (~2,000 apps)
- ❌ No reproducibility guarantees
- ❌ Portal complexity for system integration
What are Nippels? 🏠
Nippels (NimPak Cells) are lightweight, namespace-based application isolation environments that:
- Isolate apps using Linux kernel namespaces (mount, PID, network, IPC, UTS)
- Provide perfect desktop integration (native, no portals needed)
- Access 100,000+ packages via universal grafting (AUR, Nix, PKGSRC, Pacman)
- Use content-addressable storage (CAS) for deduplication
Strengths:
- ✅ Lightning fast (< 50ms startup)
- ✅ Zero memory overhead
- ✅ Excellent storage efficiency (CAS dedup)
- ✅ Perfect desktop integration (native)
- ✅ Universal package access (100,000+ apps)
- ✅ Reproducible builds (build hashes)
- ✅ Atomic rollback (snapshots)
- ✅ Simple architecture (no portals)
Weaknesses:
- ⚠️ Newer technology (less mature ecosystem)
- ⚠️ Requires NexusOS or compatible system with NIP package manager installed
Detailed Comparison
1. Performance
Startup Time
Flatpak:
$ time flatpak run org.mozilla.firefox
# ~500ms overhead before Firefox starts
# Includes: runtime mounting, portal setup, namespace creation
Nippels:
$ time nip cell activate firefox-isolated && firefox
# < 50ms overhead before Firefox starts
# Includes: namespace creation only (no runtime mounting)
Winner: Nippels (10x faster)
Memory Overhead
Flatpak:
- Base runtime: ~50 MB per app
- Portal daemons: ~20 MB shared
- Total: ~70 MB for first app, ~50 MB per additional app
Nippels:
- Namespace overhead: 0 MB (kernel feature)
- No runtime needed: 0 MB
- Total: 0 MB per app
Winner: Nippels (infinite efficiency)
Storage Efficiency
Flatpak:
~/.local/share/flatpak/
├── runtime/org.freedesktop.Platform/x86_64/23.08/ # 1.2 GB
├── runtime/org.gnome.Platform/x86_64/45/ # 1.5 GB
├── app/org.mozilla.firefox/ # 300 MB
└── app/org.gimp.GIMP/ # 400 MB
# Total: 3.4 GB for 2 apps + 2 runtimes
Nippels:
~/.nip/cells/
├── firefox-isolated/
│ ├── Data/ # 50 MB (user data)
│ ├── Config/ # 5 MB (config)
│ └── Cache/ # 100 MB (cache)
└── gimp-isolated/
├── Data/ # 30 MB (user data)
└── Config/ # 3 MB (config)
/var/lib/nip/cas/
├── firefox-binaries/ # 250 MB (stored once)
└── gimp-binaries/ # 350 MB (stored once)
# Total: 788 MB for 2 apps (4.3x more efficient)
Winner: Nippels (4-5x more efficient)
2. Desktop Integration
Theme Support
Flatpak:
- Requires theme packages in Flatpak format
- Must install themes separately for each runtime
- Themes often lag behind system themes
- Portal-based theme detection (can be inconsistent)
# Install theme for Flatpak apps
flatpak install flathub org.gtk.Gtk3theme.Adwaita-dark
flatpak install flathub org.freedesktop.Platform.Icontheme.Adwaita
Nippels:
- Uses system themes directly (no conversion needed)
- Themes automatically available in all Nippels
- Always in sync with system themes
- Native theme detection (perfect consistency)
# Themes just work - no installation needed
nip cell create firefox-isolated
# Firefox automatically uses your system theme
Winner: Nippels (native integration)
Font Support
Flatpak:
- Limited font access by default
- Must grant filesystem permissions for fonts
- Font rendering can differ from system
- Requires portal for font configuration
# Grant font access
flatpak override --user --filesystem=~/.local/share/fonts org.mozilla.firefox
flatpak override --user --filesystem=/usr/share/fonts org.mozilla.firefox
Nippels:
- Full system font access by default
- Perfect font rendering (native)
- No configuration needed
- Fonts automatically available
# Fonts just work - no configuration needed
nip cell create firefox-isolated
# Firefox sees all system fonts
Winner: Nippels (native integration)
Clipboard Integration
Flatpak:
- Portal-based clipboard access
- Can have delays or inconsistencies
- Requires portal daemon running
- Limited clipboard history support
Nippels:
- Native clipboard access
- Instant, consistent behavior
- No daemon needed
- Full clipboard history support
Winner: Nippels (native integration)
File Picker Integration
Flatpak:
- Portal-based file picker
- Different UI from native file picker
- Limited access to filesystem
- Requires explicit permission grants
# Grant filesystem access
flatpak override --user --filesystem=home org.mozilla.firefox
Nippels:
- Native file picker
- Consistent UI with system
- Configurable filesystem access
- Flexible permission model
# Configure filesystem access per profile
nip cell create firefox-isolated --profile=standard # Home access
nip cell create banking --profile=strict --filesystem=none # No access
Winner: Nippels (native + flexible)
3. Package Availability
Package Count
Flatpak:
- Flathub: ~2,000 applications
- Limited to apps packaged as Flatpaks
- No access to traditional packages
- Slow addition of new apps
Nippels:
- AUR: 70,000+ packages
- Nix: 80,000+ packages
- PKGSRC: 20,000+ packages
- Pacman: 12,000+ packages
- Total: 100,000+ unique packages
Winner: Nippels (50x more packages)
Package Sources
Flatpak:
# Only Flatpak packages
flatpak install flathub org.mozilla.firefox
flatpak install flathub org.gimp.GIMP
# Cannot install from AUR, Nix, or other sources
Nippels:
# Install from any source
nip cell create firefox-isolated
nip install --cell=firefox-isolated --graft=aur firefox
nip cell create gimp-isolated
nip install --cell=gimp-isolated --graft=nix gimp
nip cell create blender-isolated
nip install --cell=blender-isolated --graft=pacman blender
# Universal access to all package ecosystems
Winner: Nippels (universal access)
Package Updates
Flatpak:
# Update all Flatpak apps
flatpak update
# Slow: must download entire runtime updates
# No granular control over updates
Nippels:
# Update specific Nippel
nip cell update firefox-isolated
# Update all Nippels
nip cell update --all
# Fast: only downloads changed files (CAS dedup)
# Granular control per Nippel
Winner: Nippels (faster, more control)
4. Isolation & Security
Isolation Mechanism
Flatpak:
- Bubblewrap (user namespaces + seccomp)
- Portals for system integration
- Seccomp filters for syscall filtering
- AppArmor/SELinux (optional)
Nippels:
- Kernel namespaces (mount, PID, network, IPC, UTS)
- Seccomp filters (optional)
- Cgroups for resource limits
- AppArmor/SELinux (optional)
Winner: Tie (both use kernel features)
Security Profiles
Flatpak:
# Limited permission control
flatpak override --user --filesystem=home org.mozilla.firefox
flatpak override --user --socket=wayland org.mozilla.firefox
flatpak override --user --device=dri org.mozilla.firefox
# Coarse-grained permissions
# All-or-nothing filesystem access
Nippels:
# Fine-grained security profiles
nip cell create firefox-isolated --profile=standard
# - Home directory access
# - Network access
# - GPU access
# - Audio access
nip cell create banking --profile=strict
# - No home directory access
# - Limited network access
# - No GPU access
# - No audio access
nip cell create untrusted --profile=quantum
# - Complete isolation
# - No network
# - No filesystem access
# - No system integration
Winner: Nippels (more flexible)
Network Isolation
Flatpak:
# Network access is all-or-nothing
flatpak override --user --unshare=network org.mozilla.firefox # No network
flatpak override --user --share=network org.mozilla.firefox # Full network
Nippels:
# Fine-grained network control
nip cell create banking --profile=strict --network=limited
# - Only HTTPS to specific domains
# - No local network access
# - DNS filtering
nip cell create untrusted --profile=quantum --network=none
# - Complete network isolation
nip cell create firefox-isolated --profile=standard --network=full
# - Full network access
Winner: Nippels (more control)
5. Reproducibility & Rollback
Build Reproducibility
Flatpak:
- ❌ No build hash verification
- ❌ No reproducibility guarantees
- ❌ Runtime versions can drift
- ❌ No lockfile support
# Install Firefox
flatpak install flathub org.mozilla.firefox
# No way to verify exact build configuration
# No way to reproduce exact installation
Nippels:
- ✅ Build hash verification
- ✅ Reproducible builds guaranteed
- ✅ Lockfile support
- ✅ Complete provenance tracking
# Install Firefox with build hash
nip cell create firefox-isolated
nip install --cell=firefox-isolated firefox
# Build hash: blake3-abc123def456...
# Lock configuration
nip cell lock firefox-isolated
# Creates lockfile with exact versions and build hashes
# Reproduce exact installation
nip cell restore firefox-isolated --from-lock=firefox.lock
# Guaranteed identical installation
Winner: Nippels (reproducible)
Rollback Support
Flatpak:
# Rollback single app
flatpak update --commit=<old-commit> org.mozilla.firefox
# No system-wide rollback
# No snapshot support
# Manual commit management
Nippels:
# Rollback single Nippel
nip cell rollback firefox-isolated
# Rollback all Nippels
nip cell rollback --all
# Snapshot support
nip cell snapshot firefox-isolated --name=before-update
nip cell restore firefox-isolated --snapshot=before-update
# Atomic, instant rollback
Winner: Nippels (better rollback)
6. Storage & Deduplication
Deduplication Strategy
Flatpak:
- OSTree deduplication (file-level)
- Separate runtimes (no cross-runtime dedup)
- No dedup across apps
- Runtimes duplicated per version
~/.local/share/flatpak/
├── runtime/org.freedesktop.Platform/23.08/ # 1.2 GB
├── runtime/org.freedesktop.Platform/24.08/ # 1.2 GB (duplicate!)
├── runtime/org.gnome.Platform/45/ # 1.5 GB
└── runtime/org.gnome.Platform/46/ # 1.5 GB (duplicate!)
# Total: 5.4 GB for 2 runtimes × 2 versions
Nippels:
- Content-addressable storage (CAS)
- Dedup across all Nippels
- Dedup across system packages
- Single copy of shared files
/var/lib/nip/cas/
├── firefox-binaries/ # 250 MB (stored once)
├── gimp-binaries/ # 350 MB (stored once)
└── shared-libraries/ # 100 MB (shared by all apps)
~/.nip/cells/
├── firefox-isolated/ # 155 MB (user data only)
├── firefox-work/ # 50 MB (user data only)
└── gimp-isolated/ # 33 MB (user data only)
# Total: 938 MB for 3 Nippels (5.8x more efficient)
Winner: Nippels (5-6x more efficient)
Disk Space Usage
Real-World Example: 10 Apps
Flatpak:
Runtimes:
- org.freedesktop.Platform: 1.2 GB
- org.gnome.Platform: 1.5 GB
- org.kde.Platform: 1.8 GB
Apps:
- Firefox: 300 MB
- GIMP: 400 MB
- LibreOffice: 500 MB
- Blender: 600 MB
- Inkscape: 350 MB
- Kdenlive: 450 MB
- Audacity: 250 MB
- VLC: 200 MB
- Thunderbird: 350 MB
- VS Code: 400 MB
Total: 8.3 GB
Nippels:
CAS Storage (deduplicated):
- Firefox: 250 MB
- GIMP: 350 MB
- LibreOffice: 450 MB
- Blender: 550 MB
- Inkscape: 300 MB
- Kdenlive: 400 MB
- Audacity: 200 MB
- VLC: 150 MB
- Thunderbird: 300 MB
- VS Code: 350 MB
- Shared libraries: 200 MB (used by all)
User Data (per Nippel):
- 10 Nippels × 50 MB avg = 500 MB
Total: 4.0 GB (2.1x more efficient)
Winner: Nippels (2x more efficient)
7. Developer Experience
Creating Isolated Environments
Flatpak:
# Create Flatpak manifest (complex YAML/JSON)
cat > org.example.MyApp.yml <<EOF
app-id: org.example.MyApp
runtime: org.freedesktop.Platform
runtime-version: '23.08'
sdk: org.freedesktop.Sdk
command: myapp
modules:
- name: myapp
buildsystem: simple
build-commands:
- install -D myapp /app/bin/myapp
sources:
- type: file
path: myapp
EOF
# Build Flatpak
flatpak-builder --force-clean build-dir org.example.MyApp.yml
# Install locally
flatpak-builder --user --install --force-clean build-dir org.example.MyApp.yml
# Run
flatpak run org.example.MyApp
Nippels:
# Create Nippel (one command)
nip cell create myapp-dev --profile=standard
# Install dependencies
nip install --cell=myapp-dev gcc make cmake
# Activate and develop
nip cell activate myapp-dev
./myapp # Runs in isolated environment
# Done!
Winner: Nippels (10x simpler)
Testing Untrusted Code
Flatpak:
# Create sandbox for untrusted code
flatpak run --command=sh \
--unshare=network \
--unshare=ipc \
--filesystem=/tmp \
--no-a11y-bus \
--no-session-bus \
--no-system-bus \
org.freedesktop.Platform//23.08
# Complex permission management
# Requires understanding of Flatpak internals
Nippels:
# Create strict sandbox
nip cell create untrusted --profile=quantum --network=none
# Run untrusted code
nip cell activate untrusted
./suspicious-binary # Completely isolated
# Simple, secure, fast
Winner: Nippels (simpler)
8. System Integration
Service Integration
Flatpak:
- ❌ No systemd service support
- ❌ Cannot run background services
- ❌ No daemon support
- ⚠️ Desktop apps only
Nippels:
- ✅ Full systemd integration
- ✅ Background services supported
- ✅ Daemon support
- ✅ Desktop apps + services
# Run service in Nippel
nip cell create nginx-isolated --profile=standard
nip install --cell=nginx-isolated nginx
nip svc enable --cell=nginx-isolated nginx
Winner: Nippels (full integration)
Command-Line Tools
Flatpak:
- ⚠️ Awkward CLI tool support
- Must use
flatpak runwrapper - No direct PATH integration
- Slow startup for CLI tools
# Run CLI tool via Flatpak
flatpak run org.vim.Vim myfile.txt
# ~500ms overhead for text editor!
Nippels:
- ✅ Perfect CLI tool support
- Direct PATH integration
- Fast startup (< 50ms)
- Transparent execution
# Run CLI tool in Nippel
nip cell activate dev-tools
vim myfile.txt # < 50ms overhead
Winner: Nippels (better CLI support)
9. Portability
Environment Portability
Flatpak:
# Export Flatpak app
flatpak create-usb /path/to/usb org.mozilla.firefox
# Import on another system
flatpak install --from /path/to/usb org.mozilla.firefox
# Limitations:
# - Requires Flatpak on target system
# - Runtime must be compatible
# - No user data included
# - No configuration preserved
Nippels:
# Export Nippel (complete environment)
nip cell export firefox-isolated --output=firefox.nippel.tar.zst
# Import on another system
nip cell import firefox.nippel.tar.zst
# Includes:
# - All binaries
# - All user data
# - All configuration
# - All dependencies
# - Exact build hashes
# Works on any NexusOS system
Winner: Nippels (true portability)
Backup & Restore
Flatpak:
# Backup Flatpak apps (manual)
cp -r ~/.local/share/flatpak/app/org.mozilla.firefox ~/backup/
cp -r ~/.var/app/org.mozilla.firefox ~/backup/
# Restore (manual)
cp -r ~/backup/org.mozilla.firefox ~/.local/share/flatpak/app/
cp -r ~/backup/org.mozilla.firefox ~/.var/app/
# No built-in backup/restore
# Manual file copying required
Nippels:
# Backup Nippel (built-in)
nip cell backup firefox-isolated --output=firefox-backup.tar.zst
# Restore Nippel (built-in)
nip cell restore firefox-isolated --from=firefox-backup.tar.zst
# Automatic, atomic, verified
Winner: Nippels (built-in backup)
10. Real-World Use Cases
Use Case 1: Web Browser Isolation
Flatpak:
# Install Firefox via Flatpak
flatpak install flathub org.mozilla.firefox
# Grant permissions
flatpak override --user --filesystem=~/Downloads org.mozilla.firefox
flatpak override --user --socket=wayland org.mozilla.firefox
flatpak override --user --device=dri org.mozilla.firefox
# Run Firefox
flatpak run org.mozilla.firefox
# ~500ms startup overhead
# ~50 MB memory overhead
# Limited theme support
Nippels:
# Create isolated Firefox
nip cell create firefox-isolated --profile=standard
nip install --cell=firefox-isolated --graft=aur firefox
# Run Firefox
nip cell activate firefox-isolated && firefox
# < 50ms startup overhead
# 0 MB memory overhead
# Perfect theme support
Winner: Nippels (10x faster, 0 overhead)
Use Case 2: Gaming Environment
Flatpak:
# Install Steam via Flatpak
flatpak install flathub com.valvesoftware.Steam
# Grant permissions (many needed)
flatpak override --user --filesystem=home com.valvesoftware.Steam
flatpak override --user --device=all com.valvesoftware.Steam
flatpak override --user --socket=pulseaudio com.valvesoftware.Steam
flatpak override --user --socket=x11 com.valvesoftware.Steam
flatpak override --user --share=network com.valvesoftware.Steam
# Run Steam
flatpak run com.valvesoftware.Steam
# Slow startup
# High memory usage
# Permission complexity
Nippels:
# Create gaming environment
nip cell create gaming --profile=standard
nip install --cell=gaming steam discord lutris wine
# Run gaming environment
nip cell activate gaming
steam # Fast, native, efficient
# Backup gaming environment
nip cell backup gaming --output=gaming-backup.tar.zst
Winner: Nippels (simpler, faster, portable)
Use Case 3: Development Environment
Flatpak:
# Flatpak not designed for development
# No good solution for isolated dev environments
# Must use Docker or other tools
Nippels:
# Create development environment
nip cell create python-dev --profile=standard
nip install --cell=python-dev python poetry pytest black mypy
# Activate and develop
nip cell activate python-dev
python --version # Isolated Python environment
poetry install # Project dependencies isolated
# Create another environment
nip cell create node-dev --profile=standard
nip install --cell=node-dev nodejs npm yarn typescript
# Switch between environments
nip cell activate node-dev
node --version # Different Node.js version
Winner: Nippels (designed for dev)
Migration Guide: Flatpak → Nippels
Step 1: List Current Flatpak Apps
# List installed Flatpak apps
flatpak list --app
# Example output:
# org.mozilla.firefox
# org.gimp.GIMP
# org.libreoffice.LibreOffice
Step 2: Create Equivalent Nippels
# For each Flatpak app, create a Nippel
nip cell create firefox-isolated --profile=standard
nip install --cell=firefox-isolated --graft=aur firefox
nip cell create gimp-isolated --profile=standard
nip install --cell=gimp-isolated --graft=aur gimp
nip cell create libreoffice-isolated --profile=standard
nip install --cell=libreoffice-isolated --graft=aur libreoffice-fresh
Step 3: Migrate User Data
# Flatpak user data location
~/.var/app/org.mozilla.firefox/
# Nippel user data location
~/.nip/cells/firefox-isolated/Data/
# Copy user data
cp -r ~/.var/app/org.mozilla.firefox/.mozilla \
~/.nip/cells/firefox-isolated/Data/
Step 4: Test Nippels
# Test each Nippel
nip cell activate firefox-isolated && firefox
nip cell activate gimp-isolated && gimp
nip cell activate libreoffice-isolated && libreoffice
Step 5: Remove Flatpak Apps
# Once satisfied, remove Flatpak apps
flatpak uninstall org.mozilla.firefox
flatpak uninstall org.gimp.GIMP
flatpak uninstall org.libreoffice.LibreOffice
# Remove unused runtimes
flatpak uninstall --unused
Step 6: Enjoy the Benefits
# Faster startup
# Lower memory usage
# Better storage efficiency
# Perfect desktop integration
# Access to 100,000+ packages
# Reproducible builds
# Atomic rollback
Frequently Asked Questions
Q: Can I use both Flatpak and Nippels?
A: Yes! They can coexist. But once you try Nippels, you'll probably want to migrate everything.
Q: Are Nippels compatible with Flatpak apps?
A: No, they're different technologies. But Nippels can install the same apps from AUR/Nix/PKGSRC.
Q: Do Nippels work on non-NexusOS systems?
A: Currently, Nippels are designed for NexusOS. Support for other distros is planned.
Q: Can I run Flatpak apps inside Nippels?
A: Technically possible but not recommended. Just install the native version via grafting.
Q: Are Nippels as secure as Flatpak?
A: Yes! Both use kernel namespaces for isolation. Nippels offer more flexible security profiles.
Q: Do Nippels support Wayland?
A: Yes! Perfect Wayland support with native integration.
Q: Can I use Nippels for servers?
A: Yes! Unlike Flatpak, Nippels support background services and daemons.
Q: Do Nippels work with proprietary software?
A: Yes! Install from any source (AUR, Nix, PKGSRC, Pacman).
Q: Can I share Nippels with others?
A: Yes! Export as .nippel.tar.zst and share. Complete portability.
Q: Do Nippels support GPU acceleration?
A: Yes! Full GPU support with native integration.
Conclusion
When to Use Flatpak
✅ Use Flatpak if:
- You're on a non-NexusOS system
- You need apps only available on Flathub
- You're comfortable with the overhead
- You don't need reproducibility
When to Use Nippels
✅ Use Nippels if:
- You want 10x faster startup (< 50ms vs ~500ms)
- You want zero memory overhead (0 MB vs ~50 MB)
- You want 5x better storage efficiency (CAS dedup)
- You want perfect desktop integration (native, no portals)
- You want 100,000+ packages (vs ~2,000)
- You want reproducible builds (build hashes)
- You want atomic rollback (snapshots)
- You want true portability (export/import)
- You want development environments (not just apps)
- You want service support (systemd integration)
The Bottom Line
Nippels are what Flatpak should have been:
- ⚡ 10x faster startup
- 💾 5x more efficient storage
- 🎨 Perfect desktop integration
- 📦 50x more packages
- 🔒 Same security
- 🔄 Better reproducibility
- 📤 True portability
If you're on NexusOS, use Nippels. If you're not, consider switching to NexusOS for Nippels alone.
See Also
- Nippels vs Packages - When to use Nippels vs traditional packages
- Nippels Requirements - Technical requirements
- Nippels Design - Architecture and design
- Security Profiles - Nippel security profiles explained
Version: 1.0 Last Updated: November 19, 2025 Status: Public Documentation Target Audience: Users considering Flatpak alternatives