system update: general fixes to flatpak parsing

core/internal/server/sysupdate/backend_apt.go

@@ -45,7 +45,11 @@ func (aptBackend) Upgrade(ctx context.Context, opts UpgradeOptions, onLine func(
 			OnLine: onLine,
 		})
 	}
-	argv := []string{"pkexec", "env", "DEBIAN_FRONTEND=noninteractive", "LC_ALL=C", bin, "upgrade", "-y"}
+	names := pickTargetNames(opts.Targets, "apt", true)
+	if len(names) == 0 {
+		return nil
+	}
+	argv := append([]string{"pkexec", "env", "DEBIAN_FRONTEND=noninteractive", "LC_ALL=C", bin, "install", "-y", "--only-upgrade"}, names...)
 	return Run(ctx, argv, RunOptions{OnLine: onLine})
 }
 

core/internal/server/sysupdate/backend_dnf.go

@@ -45,7 +45,12 @@ func (b dnfBackend) Upgrade(ctx context.Context, opts UpgradeOptions, onLine fun
 	if opts.DryRun {
 		return Run(ctx, []string{b.bin, "upgrade", "--assumeno"}, RunOptions{OnLine: onLine})
 	}
-	return Run(ctx, []string{"pkexec", b.bin, "upgrade", "-y"}, RunOptions{OnLine: onLine})
+	names := pickTargetNames(opts.Targets, b.bin, true)
+	if len(names) == 0 {
+		return nil
+	}
+	argv := append([]string{"pkexec", b.bin, "upgrade", "-y"}, names...)
+	return Run(ctx, argv, RunOptions{OnLine: onLine})
 }
 
 func dnfListUpgrades(ctx context.Context, bin string) (string, error) {
@@ -88,14 +93,14 @@ func parseDnfList(text, backendID string, installed map[string]string) []Package
 		}
 		nameArch := fields[0]
 		version := fields[1]
-		switch nameArch {
+		dot := strings.LastIndex(nameArch, ".")
-		case "Available", "Upgrades":
+		if dot <= 0 {
 			continue
 		}
-		name := nameArch
+		if !looksLikeRpmVersion(version) {
-		if dot := strings.LastIndex(nameArch, "."); dot > 0 {
+			continue
-			name = nameArch[:dot]
 		}
+		name := nameArch[:dot]
 		pkgs = append(pkgs, Package{
 			Name:        nameArch,
 			Repo:        RepoSystem,
@@ -106,3 +111,15 @@ func parseDnfList(text, backendID string, installed map[string]string) []Package
 	}
 	return pkgs
 }
+
+func looksLikeRpmVersion(s string) bool {
+	if s == "" {
+		return false
+	}
+	for _, r := range s {
+		if r >= '0' && r <= '9' {
+			return true
+		}
+	}
+	return false
+}

core/internal/server/sysupdate/backend_dnf_test.go

@@ -56,12 +56,15 @@ bash.x86_64       5.2.40-1.fc41       updates`,
 			want:      nil,
 		},
 		{
-			name:      "package without arch suffix",
+			name: "skips dnf5 banner / column header lines",
-			input:     "noarchpkg 1.2.3 updates",
+			input: `Updates available
+Last metadata expiration check: 0:01:23 ago on Tue Apr 29 14:00:00 2026.
+Package    Version    Repository    Size
+bash.x86_64       5.2.40-1.fc41       updates`,
 			backendID: "dnf",
-			installed: map[string]string{"noarchpkg": "1.2.0"},
+			installed: nil,
 			want: []Package{
-				{Name: "noarchpkg", Repo: RepoSystem, Backend: "dnf", FromVersion: "1.2.0", ToVersion: "1.2.3"},
+				{Name: "bash.x86_64", Repo: RepoSystem, Backend: "dnf", FromVersion: "", ToVersion: "5.2.40-1.fc41"},
 			},
 		},
 	}

core/internal/server/sysupdate/backend_flatpak.go

@@ -70,13 +70,32 @@ type flatpakInstalledEntry struct {
 }
 
 func (flatpakBackend) Upgrade(ctx context.Context, opts UpgradeOptions, onLine func(string)) error {
-	argv := []string{"flatpak", "update", "-y", "--noninteractive"}
 	if opts.DryRun {
-		argv = []string{"flatpak", "update", "--no-deploy", "-y"}
+		return Run(ctx, []string{"flatpak", "update", "--no-deploy", "-y"}, RunOptions{OnLine: onLine})
 	}
+	refs := flatpakTargetRefs(opts.Targets)
+	if len(refs) == 0 {
+		return nil
+	}
+	argv := append([]string{"flatpak", "update", "-y", "--noninteractive"}, refs...)
 	return Run(ctx, argv, RunOptions{OnLine: onLine})
 }
 
+func flatpakTargetRefs(targets []Package) []string {
+	out := make([]string, 0, len(targets))
+	for _, p := range targets {
+		if p.Backend != "flatpak" {
+			continue
+		}
+		ref := p.Ref
+		if ref == "" {
+			ref = p.Name
+		}
+		out = append(out, ref)
+	}
+	return out
+}
+
 func parseFlatpakUpdates(text string, installed map[string]flatpakInstalledEntry) []Package {
 	if text == "" {
 		return nil
@@ -111,14 +130,25 @@ func parseFlatpakUpdates(text string, installed map[string]flatpakInstalledEntry
 			key = appID + "//" + branch
 		}
 		inst := installed[key]
+
+		if inst.commit != "" && commit != "" && strings.HasPrefix(commit, inst.commit) {
+			continue
+		}
+
 		from, to := flatpakVersionPair(inst.version, inst.commit, version, commit)
 
+		ref := appID
+		if branch != "" {
+			ref = appID + "//" + branch
+		}
+
 		pkgs = append(pkgs, Package{
 			Name:        display,
 			Repo:        RepoFlatpak,
 			Backend:     "flatpak",
 			FromVersion: from,
 			ToVersion:   to,
+			Ref:         ref,
 		})
 	}
 	return pkgs

core/internal/server/sysupdate/backend_flatpak_test.go

@@ -31,6 +31,7 @@ func TestParseFlatpakUpdates(t *testing.T) {
 					Backend:     "flatpak",
 					FromVersion: "8b16fa1a",
 					ToVersion:   "43a1e5d2",
+					Ref:         "com.discordapp.Discord//stable",
 				},
 			},
 		},
@@ -47,6 +48,7 @@ func TestParseFlatpakUpdates(t *testing.T) {
 					Backend:     "flatpak",
 					FromVersion: "1.4.2",
 					ToVersion:   "1.5.0",
+					Ref:         "com.example.App//stable",
 				},
 			},
 		},
@@ -61,6 +63,7 @@ func TestParseFlatpakUpdates(t *testing.T) {
 					Backend:     "flatpak",
 					FromVersion: "",
 					ToVersion:   "badcd4af",
+					Ref:         "org.gnome.Platform//49",
 				},
 			},
 		},
@@ -74,6 +77,7 @@ func TestParseFlatpakUpdates(t *testing.T) {
 					Backend:     "flatpak",
 					FromVersion: "",
 					ToVersion:   "2.0",
+					Ref:         "com.example.NoName//stable",
 				},
 			},
 		},
@@ -87,9 +91,18 @@ func TestParseFlatpakUpdates(t *testing.T) {
 					Backend:     "flatpak",
 					FromVersion: "",
 					ToVersion:   "1.0",
+					Ref:         "org.real.App//stable",
 				},
 			},
 		},
+		{
+			name:  "skips phantom updates where remote commit matches installed",
+			input: "com.phantom.App\t\tstable\tabc12345deadbeef\tPhantom",
+			installed: map[string]flatpakInstalledEntry{
+				"com.phantom.App//stable": {commit: "abc12345"},
+			},
+			want: nil,
+		},
 	}
 
 	for _, tt := range tests {

core/internal/server/sysupdate/backend_pacman.go

@@ -43,17 +43,24 @@ func (b pacmanBackend) Upgrade(ctx context.Context, opts UpgradeOptions, onLine
 	if opts.DryRun {
 		return Run(ctx, []string{"pacman", "-Sup"}, RunOptions{OnLine: onLine})
 	}
-	return Run(ctx, []string{"pkexec", "pacman", "-Syu", "--noconfirm"}, RunOptions{OnLine: onLine})
+	names := pickTargetNames(opts.Targets, b.ID(), opts.IncludeAUR)
+	if len(names) == 0 {
+		return nil
+	}
+	argv := append([]string{"pkexec", "pacman", "-Sy", "--noconfirm", "--needed"}, names...)
+	return Run(ctx, argv, RunOptions{OnLine: onLine})
 }
 
 type archHelperBackend struct {
 	id string
 }
 
-func (b archHelperBackend) ID() string                         { return b.id }
+func (b archHelperBackend) ID() string      { return b.id }
-func (b archHelperBackend) Repo() RepoKind                     { return RepoSystem }
+func (b archHelperBackend) Repo() RepoKind  { return RepoSystem }
-func (b archHelperBackend) NeedsAuth() bool                    { return true }
+func (b archHelperBackend) NeedsAuth() bool { return true }
-func (b archHelperBackend) RunsInTerminal() bool               { return true }
+func (b archHelperBackend) RunsInTerminal() bool {
+	return os.Getenv("DMS_FORCE_PKEXEC") != "1"
+}
 func (b archHelperBackend) IsAvailable(_ context.Context) bool { return commandExists(b.id) }
 
 func (b archHelperBackend) DisplayName() string {
@@ -86,18 +93,37 @@ func (b archHelperBackend) Upgrade(ctx context.Context, opts UpgradeOptions, onL
 	if opts.DryRun {
 		return Run(ctx, []string{b.id, "-Sup"}, RunOptions{OnLine: onLine})
 	}
+	names := pickTargetNames(opts.Targets, b.id, opts.IncludeAUR)
+	if len(names) == 0 {
+		return nil
+	}
+	if os.Getenv("DMS_FORCE_PKEXEC") == "1" {
+		argv := append([]string{"pkexec", b.id, "-Sy", "--noconfirm", "--needed"}, names...)
+		return Run(ctx, argv, RunOptions{OnLine: onLine})
+	}
 	term := findTerminal(opts.Terminal)
 	if term == "" {
 		return fmt.Errorf("no terminal found (pick one in DMS settings, set $TERMINAL, or install kitty/ghostty/foot/alacritty)")
 	}
-	cmd := fmt.Sprintf("%s -Syu", b.id)
+	cmd := fmt.Sprintf("%s -Sy --noconfirm --needed %s", b.id, strings.Join(names, " "))
-	if !opts.IncludeAUR {
-		cmd += " --repo"
-	}
 	title := fmt.Sprintf("DMS — System Update (%s)", b.id)
 	return Run(ctx, wrapInTerminal(term, title, cmd), RunOptions{OnLine: onLine})
 }
 
+func pickTargetNames(targets []Package, backendID string, includeAUR bool) []string {
+	out := make([]string, 0, len(targets))
+	for _, p := range targets {
+		if p.Backend != backendID {
+			continue
+		}
+		if !includeAUR && p.Repo == RepoAUR {
+			continue
+		}
+		out = append(out, p.Name)
+	}
+	return out
+}
+
 func pacmanRepoUpdates(ctx context.Context) (string, error) {
 	if commandExists("checkupdates") {
 		return capturePermissive(ctx, "checkupdates")

core/internal/server/sysupdate/backend_zypper.go

@@ -74,5 +74,10 @@ func (zypperBackend) Upgrade(ctx context.Context, opts UpgradeOptions, onLine fu
 	if opts.DryRun {
 		return Run(ctx, []string{"zypper", "--non-interactive", "--dry-run", "update"}, RunOptions{OnLine: onLine})
 	}
-	return Run(ctx, []string{"pkexec", "zypper", "--non-interactive", "update"}, RunOptions{OnLine: onLine})
+	names := pickTargetNames(opts.Targets, "zypper", true)
+	if len(names) == 0 {
+		return nil
+	}
+	argv := append([]string{"pkexec", "zypper", "--non-interactive", "update"}, names...)
+	return Run(ctx, argv, RunOptions{OnLine: onLine})
 }

core/internal/server/sysupdate/executor.go

@@ -8,6 +8,7 @@ import (
 	"os"
 	"os/exec"
 	"sync"
+	"syscall"
 )
 
 type RunOptions struct {
@@ -24,6 +25,13 @@ func Run(ctx context.Context, argv []string, opts RunOptions) error {
 	if len(opts.Env) > 0 {
 		cmd.Env = append(cmd.Environ(), opts.Env...)
 	}
+	cmd.SysProcAttr = &syscall.SysProcAttr{Setpgid: true}
+	cmd.Cancel = func() error {
+		if cmd.Process == nil {
+			return nil
+		}
+		return syscall.Kill(-cmd.Process.Pid, syscall.SIGKILL)
+	}
 
 	stdout, err := cmd.StdoutPipe()
 	if err != nil {

core/internal/server/sysupdate/manager.go

@@ -309,6 +309,12 @@ func (m *Manager) runUpgrade(ctx context.Context, opts UpgradeOptions) {
 		return
 	}
 
+	if len(opts.Targets) == 0 {
+		m.mu.RLock()
+		opts.Targets = append([]Package(nil), m.state.Packages...)
+		m.mu.RUnlock()
+	}
+
 	opID := fmt.Sprintf("op-%d", time.Now().UnixNano())
 	m.mu.Lock()
 	m.state.Phase = PhaseUpgrading

core/internal/server/sysupdate/types.go

@@ -38,6 +38,7 @@ type Package struct {
 	ToVersion    string   `json:"toVersion,omitempty"`
 	SizeBytes    int64    `json:"sizeBytes,omitempty"`
 	ChangelogURL string   `json:"changelogUrl,omitempty"`
+	Ref          string   `json:"-"`
 }
 
 type BackendInfo struct {
@@ -77,6 +78,7 @@ type UpgradeOptions struct {
 	DryRun         bool
 	CustomCommand  string
 	Terminal       string
+	Targets        []Package
 }
 
 type RefreshOptions struct {

quickshell/Modules/DankBar/Popouts/SystemUpdatePopout.qml

@@ -1,4 +1,5 @@
 import QtQuick
+import Quickshell.Wayland
 import qs.Common
 import qs.Services
 import qs.Widgets
@@ -17,6 +18,21 @@ DankPopout {
 
     property bool _reopenAfterUpgrade: false
 
+    readonly property bool polkitModalOpen: PopoutService.polkitAuthModal?.visible ?? false
+    readonly property bool anyModalOpen: polkitModalOpen
+
+    backgroundInteractive: !anyModalOpen
+
+    customKeyboardFocus: {
+        if (!shouldBeVisible)
+            return WlrKeyboardFocus.None;
+        if (anyModalOpen)
+            return WlrKeyboardFocus.None;
+        if (CompositorService.useHyprlandFocusGrab)
+            return WlrKeyboardFocus.OnDemand;
+        return WlrKeyboardFocus.Exclusive;
+    }
+
     Connections {
         target: SystemUpdateService
         function onIsUpgradingChanged() {
@@ -38,7 +54,11 @@ DankPopout {
     screen: triggerScreen
     shouldBeVisible: false
 
-    onBackgroundClicked: close()
+    onBackgroundClicked: {
+        if (anyModalOpen)
+            return;
+        close();
+    }
 
     onShouldBeVisibleChanged: {
         if (!shouldBeVisible) {
@@ -290,7 +310,7 @@ DankPopout {
                         }
                     }
                     font.pixelSize: Theme.fontSizeMedium
-                    color: SystemUpdateService.hasError ? Theme.errorText : Theme.surfaceText
+                    color: SystemUpdateService.hasError ? Theme.error : Theme.surfaceText
                     wrapMode: Text.WordWrap
                 }