diff --git a/README.md b/README.md
index 9bc59af..f780db4 100644
--- a/README.md
+++ b/README.md
@@ -104,16 +104,16 @@ All behavior shown above is driven entirely by declarative configuration.
 For the Minecraft example shown above:
 
 ```toml
-# Minecraft via mc-installer snap
-# Ubuntu: sudo snap install mc-installer
+# Prism Launcher - Minecraft launcher (Flatpak)
+# Install: flatpak install flathub org.prismlauncher.PrismLauncher
 [[entries]]
-id = "minecraft"
-label = "Minecraft"
-icon = "minecraft"
+id = "prism-launcher"
+label = "Prism Launcher"
+icon = "org.prismlauncher.PrismLauncher"
 
 [entries.kind]
-type = "snap"
-snap_name = "mc-installer"
+type = "flatpak"
+app_id = "org.prismlauncher.PrismLauncher"
 
 [entries.availability]
 [[entries.availability.windows]]
@@ -160,7 +160,7 @@ compatibility infrastructure:
 
 * Wayland and Sway
 * Rust
-* Snap
+* Flatpak and Snap
 * Proton and WINE
 
 This project was written with the assistance of generative AI-based coding
diff --git a/config.example.toml b/config.example.toml
index eded285..b86eee8 100644
--- a/config.example.toml
+++ b/config.example.toml
@@ -165,52 +165,6 @@ max_run_seconds = 0  # Unlimited
 daily_quota_seconds = 0  # Unlimited
 cooldown_seconds = 0  # No cooldown
 
-# Minecraft via mc-installer snap
-# Ubuntu: sudo snap install mc-installer
-[[entries]]
-id = "minecraft"
-label = "Minecraft"
-icon = "~/.minecraft/launcher/icons/minecraft256.png"
-
-[entries.kind]
-type = "snap"
-snap_name = "mc-installer"
-
-[entries.availability]
-[[entries.availability.windows]]
-days = "weekdays"
-start = "15:00"
-end = "18:00"
-
-[[entries.availability.windows]]
-days = "weekends"
-start = "10:00"
-end = "20:00"
-
-[entries.limits]
-max_run_seconds = 1800  # 30 minutes (roughly 3 in-game days)
-daily_quota_seconds = 3600  # 1 hour per day
-cooldown_seconds = 600  # 10 minute cooldown
-
-[[entries.warnings]]
-seconds_before = 600
-severity = "info"
-message = "10 minutes left - start wrapping up!"
-
-[[entries.warnings]]
-seconds_before = 120
-severity = "warn"
-message = "2 minutes remaining - save your game!"
-
-[[entries.warnings]]
-seconds_before = 30
-severity = "critical"
-message = "30 seconds! Save NOW!"
-
-# Entry-specific volume restrictions (overrides global)
-[entries.volume]
-max_volume = 60  # Limit volume during gaming sessions
-
 ## === Steam games ===
 # Steam can be used via Canonical's Steam snap package:
 # https://snapcraft.io/steam
@@ -267,6 +221,76 @@ days = "weekends"
 start = "10:00"
 end = "20:00"
 
+## === Flatpak-based applications ===
+# Flatpak entries use the "flatpak" type for proper process management.
+# Similar to Snap, Flatpak apps run in sandboxed environments and use
+# systemd scopes for process management.
+
+# Prism Launcher - Minecraft launcher (Flatpak)
+# Install: flatpak install flathub org.prismlauncher.PrismLauncher
+[[entries]]
+id = "prism-launcher"
+label = "Prism Launcher"
+icon = "org.prismlauncher.PrismLauncher"
+
+[entries.kind]
+type = "flatpak"
+app_id = "org.prismlauncher.PrismLauncher"
+
+[entries.availability]
+[[entries.availability.windows]]
+days = "weekdays"
+start = "15:00"
+end = "18:00"
+
+[[entries.availability.windows]]
+days = "weekends"
+start = "10:00"
+end = "20:00"
+
+[entries.limits]
+max_run_seconds = 1800  # 30 minutes (roughly 3 in-game days)
+daily_quota_seconds = 3600  # 1 hour per day
+cooldown_seconds = 600  # 10 minute cooldown
+
+[[entries.warnings]]
+seconds_before = 600
+severity = "info"
+message = "10 minutes left - start wrapping up!"
+
+[[entries.warnings]]
+seconds_before = 120
+severity = "warn"
+message = "2 minutes remaining - save your game!"
+
+[[entries.warnings]]
+seconds_before = 30
+severity = "critical"
+message = "30 seconds! Save NOW!"
+
+# Entry-specific volume restrictions (overrides global)
+[entries.volume]
+max_volume = 60  # Limit volume during gaming sessions
+
+# Krita - digital painting (Flatpak)
+# Install: flatpak install flathub org.kde.krita
+[[entries]]
+id = "krita"
+label = "Krita"
+icon = "org.kde.krita"
+
+[entries.kind]
+type = "flatpak"
+app_id = "org.kde.krita"
+
+[entries.availability]
+always = true
+
+[entries.limits]
+max_run_seconds = 0  # Unlimited
+daily_quota_seconds = 0  # Unlimited
+cooldown_seconds = 0  # No cooldown
+
 ## === Media ===
 # Just use `mpv` to play media (for now).
 # Files can be local on your system or URLs (YouTube, etc).
diff --git a/crates/shepherd-api/src/types.rs b/crates/shepherd-api/src/types.rs
index 668d649..20bb6df 100644
--- a/crates/shepherd-api/src/types.rs
+++ b/crates/shepherd-api/src/types.rs
@@ -13,6 +13,7 @@ use std::time::Duration;
 pub enum EntryKindTag {
     Process,
     Snap,
+    Flatpak,
     Vm,
     Media,
     Custom,
@@ -46,6 +47,17 @@ pub enum EntryKind {
         #[serde(default)]
         env: HashMap<String, String>,
     },
+    /// Flatpak application - uses systemd scope-based process management
+    Flatpak {
+        /// The Flatpak application ID (e.g., "org.prismlauncher.PrismLauncher")
+        app_id: String,
+        /// Additional command-line arguments
+        #[serde(default)]
+        args: Vec<String>,
+        /// Additional environment variables
+        #[serde(default)]
+        env: HashMap<String, String>,
+    },
     Vm {
         driver: String,
         #[serde(default)]
@@ -67,6 +79,7 @@ impl EntryKind {
         match self {
             EntryKind::Process { .. } => EntryKindTag::Process,
             EntryKind::Snap { .. } => EntryKindTag::Snap,
+            EntryKind::Flatpak { .. } => EntryKindTag::Flatpak,
             EntryKind::Vm { .. } => EntryKindTag::Vm,
             EntryKind::Media { .. } => EntryKindTag::Media,
             EntryKind::Custom { .. } => EntryKindTag::Custom,
diff --git a/crates/shepherd-config/src/bin/validate-config.rs b/crates/shepherd-config/src/bin/validate-config.rs
index 10c27da..7d12688 100644
--- a/crates/shepherd-config/src/bin/validate-config.rs
+++ b/crates/shepherd-config/src/bin/validate-config.rs
@@ -54,6 +54,9 @@ fn main() -> ExitCode {
                         EntryKind::Snap { snap_name, .. } => {
                             format!("snap ({})", snap_name)
                         }
+                        EntryKind::Flatpak { app_id, .. } => {
+                            format!("flatpak ({})", app_id)
+                        }
                         EntryKind::Vm { driver, .. } => {
                             format!("vm ({})", driver)
                         }
diff --git a/crates/shepherd-config/src/policy.rs b/crates/shepherd-config/src/policy.rs
index 2389e52..ce6d113 100644
--- a/crates/shepherd-config/src/policy.rs
+++ b/crates/shepherd-config/src/policy.rs
@@ -256,6 +256,7 @@ fn convert_entry_kind(raw: RawEntryKind) -> EntryKind {
     match raw {
         RawEntryKind::Process { command, args, env, cwd } => EntryKind::Process { command, args, env, cwd },
         RawEntryKind::Snap { snap_name, command, args, env } => EntryKind::Snap { snap_name, command, args, env },
+        RawEntryKind::Flatpak { app_id, args, env } => EntryKind::Flatpak { app_id, args, env },
         RawEntryKind::Vm { driver, args } => EntryKind::Vm { driver, args },
         RawEntryKind::Media { library_id, args } => EntryKind::Media { library_id, args },
         RawEntryKind::Custom { type_name, payload } => EntryKind::Custom {
diff --git a/crates/shepherd-config/src/schema.rs b/crates/shepherd-config/src/schema.rs
index d1b5370..a68b4d1 100644
--- a/crates/shepherd-config/src/schema.rs
+++ b/crates/shepherd-config/src/schema.rs
@@ -116,6 +116,17 @@ pub enum RawEntryKind {
         #[serde(default)]
         env: HashMap<String, String>,
     },
+    /// Flatpak application - uses systemd scope-based process management
+    Flatpak {
+        /// The Flatpak application ID (e.g., "org.prismlauncher.PrismLauncher")
+        app_id: String,
+        /// Additional command-line arguments
+        #[serde(default)]
+        args: Vec<String>,
+        /// Additional environment variables
+        #[serde(default)]
+        env: HashMap<String, String>,
+    },
     Vm {
         driver: String,
         #[serde(default)]
diff --git a/crates/shepherd-config/src/validation.rs b/crates/shepherd-config/src/validation.rs
index 5905f0c..27dc3de 100644
--- a/crates/shepherd-config/src/validation.rs
+++ b/crates/shepherd-config/src/validation.rs
@@ -71,6 +71,14 @@ fn validate_entry(entry: &RawEntry, config: &RawConfig) -> Vec<ValidationError>
                 });
             }
         }
+        RawEntryKind::Flatpak { app_id, .. } => {
+            if app_id.is_empty() {
+                errors.push(ValidationError::EntryError {
+                    entry_id: entry.id.clone(),
+                    message: "app_id cannot be empty".into(),
+                });
+            }
+        }
         RawEntryKind::Vm { driver, .. } => {
             if driver.is_empty() {
                 errors.push(ValidationError::EntryError {
diff --git a/crates/shepherd-host-api/src/capabilities.rs b/crates/shepherd-host-api/src/capabilities.rs
index 4d5ca22..8bfed89 100644
--- a/crates/shepherd-host-api/src/capabilities.rs
+++ b/crates/shepherd-host-api/src/capabilities.rs
@@ -59,6 +59,7 @@ impl HostCapabilities {
         let mut spawn_kinds = HashSet::new();
         spawn_kinds.insert(EntryKindTag::Process);
         spawn_kinds.insert(EntryKindTag::Snap);
+        spawn_kinds.insert(EntryKindTag::Flatpak);
         spawn_kinds.insert(EntryKindTag::Vm);
         spawn_kinds.insert(EntryKindTag::Media);
 
diff --git a/crates/shepherd-host-linux/src/adapter.rs b/crates/shepherd-host-linux/src/adapter.rs
index a8bd9dd..43b8e06 100644
--- a/crates/shepherd-host-linux/src/adapter.rs
+++ b/crates/shepherd-host-linux/src/adapter.rs
@@ -13,7 +13,7 @@ use std::time::Duration;
 use tokio::sync::mpsc;
 use tracing::{info, warn};
 
-use crate::process::{init, kill_by_command, kill_snap_cgroup, ManagedProcess};
+use crate::process::{init, kill_by_command, kill_flatpak_cgroup, kill_snap_cgroup, ManagedProcess};
 
 /// Expand `~` at the beginning of a path to the user's home directory
 fn expand_tilde(path: &str) -> String {
@@ -39,6 +39,7 @@ fn expand_args(args: &[String]) -> Vec<String> {
 struct SessionInfo {
     command_name: String,
     snap_name: Option<String>,
+    flatpak_app_id: Option<String>,
 }
 
 /// Linux host adapter
@@ -132,15 +133,15 @@ impl HostAdapter for LinuxHost {
         entry_kind: &EntryKind,
         options: SpawnOptions,
     ) -> HostResult<HostSessionHandle> {
-        // Extract argv, env, cwd, and snap_name based on entry kind
-        let (argv, env, cwd, snap_name) = match entry_kind {
+        // Extract argv, env, cwd, snap_name, and flatpak_app_id based on entry kind
+        let (argv, env, cwd, snap_name, flatpak_app_id) = match entry_kind {
             EntryKind::Process { command, args, env, cwd } => {
                 let mut argv = vec![expand_tilde(command)];
                 argv.extend(expand_args(args));
                 let expanded_cwd = cwd.as_ref().map(|c| {
                     std::path::PathBuf::from(expand_tilde(&c.to_string_lossy()))
                 });
-                (argv, env.clone(), expanded_cwd, None)
+                (argv, env.clone(), expanded_cwd, None, None)
             }
             EntryKind::Snap { snap_name, command, args, env } => {
                 // For snap apps, we need to use 'snap run <snap_name>' to launch them.
@@ -153,7 +154,13 @@ impl HostAdapter for LinuxHost {
                         argv.push(cmd.clone());
                     }
                 argv.extend(expand_args(args));
-                (argv, env.clone(), None, Some(snap_name.clone()))
+                (argv, env.clone(), None, Some(snap_name.clone()), None)
+            }
+            EntryKind::Flatpak { app_id, args, env } => {
+                // For Flatpak apps, we use 'flatpak run <app_id>' to launch them.
+                let mut argv = vec!["flatpak".to_string(), "run".to_string(), app_id.clone()];
+                argv.extend(expand_args(args));
+                (argv, env.clone(), None, None, Some(app_id.clone()))
             }
             EntryKind::Vm { driver, args } => {
                 // Construct command line from VM driver
@@ -166,13 +173,13 @@ impl HostAdapter for LinuxHost {
                         argv.push(value.to_string());
                     }
                 }
-                (argv, HashMap::new(), None, None)
+                (argv, HashMap::new(), None, None, None)
             }
             EntryKind::Media { library_id, args: _ } => {
                 // For media, we'd typically launch a media player
                 // This is a placeholder - real implementation would integrate with a player
                 let argv = vec!["xdg-open".to_string(), expand_tilde(library_id)];
-                (argv, HashMap::new(), None, None)
+                (argv, HashMap::new(), None, None, None)
             }
             EntryKind::Custom { type_name: _, payload: _ } => {
                 return Err(HostError::UnsupportedKind);
@@ -180,19 +187,24 @@ impl HostAdapter for LinuxHost {
         };
 
         // Get the command name for fallback killing
-        // For snap apps, use the snap_name (not "snap") to avoid killing unrelated processes
+        // For snap/flatpak apps, use the app name (not "snap"/"flatpak") to avoid killing unrelated processes
         let command_name = if let Some(ref snap) = snap_name {
             snap.clone()
+        } else if let Some(ref app_id) = flatpak_app_id {
+            app_id.clone()
         } else {
             argv.first().cloned().unwrap_or_default()
         };
+
+        // Determine if this is a sandboxed app (snap or flatpak)
+        let sandboxed_app_name = snap_name.clone().or_else(|| flatpak_app_id.clone());
         
         let proc = ManagedProcess::spawn(
             &argv,
             &env,
             cwd.as_ref(),
             options.log_path.clone(),
-            snap_name.clone(),
+            sandboxed_app_name,
         )?;
 
         let pid = proc.pid;
@@ -202,9 +214,10 @@ impl HostAdapter for LinuxHost {
         let session_info_entry = SessionInfo {
             command_name: command_name.clone(),
             snap_name: snap_name.clone(),
+            flatpak_app_id: flatpak_app_id.clone(),
         };
         self.session_info.lock().unwrap().insert(session_id.clone(), session_info_entry);
-        info!(session_id = %session_id, command = %command_name, snap = ?snap_name, "Tracking session info");
+        info!(session_id = %session_id, command = %command_name, snap = ?snap_name, flatpak = ?flatpak_app_id, "Tracking session info");
 
         let handle = HostSessionHandle::new(
             session_id,
@@ -238,13 +251,16 @@ impl HostAdapter for LinuxHost {
 
         match mode {
             StopMode::Graceful { timeout } => {
-                // If this is a snap app, use cgroup-based killing (most reliable)
+                // If this is a snap or flatpak app, use cgroup-based killing (most reliable)
                 if let Some(ref info) = session_info {
                     if let Some(ref snap) = info.snap_name {
                         kill_snap_cgroup(snap, nix::sys::signal::Signal::SIGTERM);
                         info!(snap = %snap, "Sent SIGTERM via snap cgroup");
+                    } else if let Some(ref app_id) = info.flatpak_app_id {
+                        kill_flatpak_cgroup(app_id, nix::sys::signal::Signal::SIGTERM);
+                        info!(flatpak = %app_id, "Sent SIGTERM via flatpak cgroup");
                     } else {
-                        // Fall back to command name for non-snap apps
+                        // Fall back to command name for non-sandboxed apps
                         kill_by_command(&info.command_name, nix::sys::signal::Signal::SIGTERM);
                         info!(command = %info.command_name, "Sent SIGTERM via command name");
                     }
@@ -262,11 +278,14 @@ impl HostAdapter for LinuxHost {
                 let start = std::time::Instant::now();
                 loop {
                     if start.elapsed() >= timeout {
-                        // Force kill after timeout using snap cgroup or command name
+                        // Force kill after timeout using snap/flatpak cgroup or command name
                         if let Some(ref info) = session_info {
                             if let Some(ref snap) = info.snap_name {
                                 kill_snap_cgroup(snap, nix::sys::signal::Signal::SIGKILL);
                                 info!(snap = %snap, "Sent SIGKILL via snap cgroup (timeout)");
+                            } else if let Some(ref app_id) = info.flatpak_app_id {
+                                kill_flatpak_cgroup(app_id, nix::sys::signal::Signal::SIGKILL);
+                                info!(flatpak = %app_id, "Sent SIGKILL via flatpak cgroup (timeout)");
                             } else {
                                 kill_by_command(&info.command_name, nix::sys::signal::Signal::SIGKILL);
                                 info!(command = %info.command_name, "Sent SIGKILL via command name (timeout)");
@@ -292,11 +311,14 @@ impl HostAdapter for LinuxHost {
                 }
             }
             StopMode::Force => {
-                // Force kill via snap cgroup or command name
+                // Force kill via snap/flatpak cgroup or command name
                 if let Some(ref info) = session_info {
                     if let Some(ref snap) = info.snap_name {
                         kill_snap_cgroup(snap, nix::sys::signal::Signal::SIGKILL);
                         info!(snap = %snap, "Sent SIGKILL via snap cgroup");
+                    } else if let Some(ref app_id) = info.flatpak_app_id {
+                        kill_flatpak_cgroup(app_id, nix::sys::signal::Signal::SIGKILL);
+                        info!(flatpak = %app_id, "Sent SIGKILL via flatpak cgroup");
                     } else {
                         kill_by_command(&info.command_name, nix::sys::signal::Signal::SIGKILL);
                         info!(command = %info.command_name, "Sent SIGKILL via command name");
diff --git a/crates/shepherd-host-linux/src/process.rs b/crates/shepherd-host-linux/src/process.rs
index 1abfbdd..e4f54bd 100644
--- a/crates/shepherd-host-linux/src/process.rs
+++ b/crates/shepherd-host-linux/src/process.rs
@@ -91,6 +91,70 @@ pub fn kill_snap_cgroup(snap_name: &str, _signal: Signal) -> bool {
     stopped_any
 }
 
+/// Kill all processes in a Flatpak app's cgroup using systemd
+/// Flatpak apps create scopes at: app-flatpak-<app_id>-<number>.scope
+/// For example: app-flatpak-org.prismlauncher.PrismLauncher-12345.scope
+/// Similar to snap apps, we use systemctl --user to manage the scopes.
+pub fn kill_flatpak_cgroup(app_id: &str, _signal: Signal) -> bool {
+    let uid = nix::unistd::getuid().as_raw();
+    let base_path = format!(
+        "/sys/fs/cgroup/user.slice/user-{}.slice/user@{}.service/app.slice",
+        uid, uid
+    );
+    
+    // Flatpak uses a different naming pattern than snap
+    // The app_id dots are preserved: app-flatpak-org.example.App-<number>.scope
+    let pattern = format!("app-flatpak-{}-", app_id);
+    
+    let base = std::path::Path::new(&base_path);
+    if !base.exists() {
+        debug!(path = %base_path, "Flatpak cgroup base path doesn't exist");
+        return false;
+    }
+    
+    let mut stopped_any = false;
+    
+    if let Ok(entries) = std::fs::read_dir(base) {
+        for entry in entries.flatten() {
+            let name = entry.file_name();
+            let name_str = name.to_string_lossy();
+            
+            if name_str.starts_with(&pattern) && name_str.ends_with(".scope") {
+                let scope_name = name_str.to_string();
+                
+                // Always use SIGKILL for flatpak apps to prevent self-restart behavior
+                // Using systemctl kill --signal=KILL sends SIGKILL to all processes in scope
+                let result = Command::new("systemctl")
+                    .args(["--user", "kill", "--signal=KILL", &scope_name])
+                    .output();
+                
+                match result {
+                    Ok(output) => {
+                        if output.status.success() {
+                            info!(scope = %scope_name, "Killed flatpak scope via systemctl SIGKILL");
+                            stopped_any = true;
+                        } else {
+                            let stderr = String::from_utf8_lossy(&output.stderr);
+                            warn!(scope = %scope_name, stderr = %stderr, "systemctl kill command failed");
+                        }
+                    }
+                    Err(e) => {
+                        warn!(scope = %scope_name, error = %e, "Failed to run systemctl");
+                    }
+                }
+            }
+        }
+    }
+    
+    if stopped_any {
+        info!(app_id = app_id, "Killed flatpak scope(s) via systemctl SIGKILL");
+    } else {
+        debug!(app_id = app_id, "No flatpak scope found to kill");
+    }
+    
+    stopped_any
+}
+
 /// Kill processes by command name using pkill
 pub fn kill_by_command(command_name: &str, signal: Signal) -> bool {
     let signal_name = match signal {
diff --git a/crates/shepherd-launcher-ui/src/tile.rs b/crates/shepherd-launcher-ui/src/tile.rs
index 51ba455..6ab3fc0 100644
--- a/crates/shepherd-launcher-ui/src/tile.rs
+++ b/crates/shepherd-launcher-ui/src/tile.rs
@@ -79,6 +79,7 @@ impl LauncherTile {
         let fallback_icon = match entry.kind_tag {
             shepherd_api::EntryKindTag::Process => "application-x-executable",
             shepherd_api::EntryKindTag::Snap => "application-x-executable",
+            shepherd_api::EntryKindTag::Flatpak => "application-x-executable",
             shepherd_api::EntryKindTag::Vm => "computer",
             shepherd_api::EntryKindTag::Media => "video-x-generic",
             shepherd_api::EntryKindTag::Custom => "applications-other",
diff --git a/scripts/lib/install.sh b/scripts/lib/install.sh
index bdc8bd3..33b659f 100755
--- a/scripts/lib/install.sh
+++ b/scripts/lib/install.sh
@@ -127,9 +127,10 @@ EOF
 install_config() {
     local user="${1:-}"
     local source_config="${2:-}"
+    local force="${3:-false}"
     
     if [[ -z "$user" ]]; then
-        die "Usage: shepherd install config --user USER [--source CONFIG]"
+        die "Usage: shepherd install config --user USER [--source CONFIG] [--force]"
     fi
     
     validate_user "$user"
@@ -161,7 +162,15 @@ install_config() {
     
     # Check if config already exists
     if maybe_sudo test -f "$dst_config"; then
-        warn "Config file already exists at $dst_config, skipping"
+        if [[ "$force" == "true" ]]; then
+            warn "Overwriting existing config at $dst_config"
+            maybe_sudo cp "$source_config" "$dst_config"
+            maybe_sudo chown "$user:$user" "$dst_config"
+            maybe_sudo chmod 0644 "$dst_config"
+            success "Overwrote user configuration for $user"
+        else
+            warn "Config file already exists at $dst_config, skipping (use --force to overwrite)"
+        fi
     else
         # Copy config file
         maybe_sudo cp "$source_config" "$dst_config"
@@ -175,9 +184,10 @@ install_config() {
 install_all() {
     local user="${1:-}"
     local prefix="${2:-$DEFAULT_PREFIX}"
+    local force="${3:-false}"
     
     if [[ -z "$user" ]]; then
-        die "Usage: shepherd install all --user USER [--prefix PREFIX]"
+        die "Usage: shepherd install all --user USER [--prefix PREFIX] [--force]"
     fi
     
     require_root
@@ -188,7 +198,7 @@ install_all() {
     install_bins "$prefix"
     install_sway_config "$prefix"
     install_desktop_entry "$prefix"
-    install_config "$user"
+    install_config "$user" "" "$force"
     
     success "Installation complete!"
     info ""
@@ -206,6 +216,7 @@ install_main() {
     local user=""
     local prefix="$DEFAULT_PREFIX"
     local source_config=""
+    local force="false"
     
     # Parse remaining arguments
     while [[ $# -gt 0 ]]; do
@@ -222,6 +233,10 @@ install_main() {
                 source_config="$2"
                 shift 2
                 ;;
+            --force|-f)
+                force="true"
+                shift
+                ;;
             *)
                 die "Unknown option: $1"
                 ;;
@@ -233,7 +248,7 @@ install_main() {
             install_bins "$prefix"
             ;;
         config)
-            install_config "$user" "$source_config"
+            install_config "$user" "$source_config" "$force"
             ;;
         sway-config)
             install_sway_config "$prefix"
@@ -242,7 +257,7 @@ install_main() {
             install_desktop_entry "$prefix"
             ;;
         all)
-            install_all "$user" "$prefix"
+            install_all "$user" "$prefix" "$force"
             ;;
         ""|help|-h|--help)
             cat <<EOF
@@ -259,6 +274,7 @@ Options:
     --user USER       Target user for config deployment (required for config/all)
     --prefix PREFIX   Installation prefix (default: $DEFAULT_PREFIX)
     --source CONFIG   Source config file (default: config.example.toml)
+    --force, -f       Overwrite existing configuration files
 
 Environment:
     DESTDIR           Installation root for packaging (default: empty)
@@ -266,6 +282,7 @@ Environment:
 Examples:
     shepherd install bins --prefix /usr/local
     shepherd install config --user kiosk
+    shepherd install config --user kiosk --force
     shepherd install all --user kiosk --prefix /usr
 EOF
             ;;