Keep Note Info open across note changes

src-tauri/src/commands.rs

@@ -331,6 +331,19 @@ pub fn set_theme(state: State<'_, AppState>, theme: String) -> Result<(), String
     Ok(())
 }
 
+#[tauri::command]
+pub fn set_system_themes(
+    state: State<'_, AppState>,
+    light: String,
+    dark: String,
+) -> Result<(), String> {
+    let mut config = state.config.lock().map_err(|e| e.to_string())?;
+    config.system_light_theme = light;
+    config.system_dark_theme = dark;
+    save_app_config(&config)?;
+    Ok(())
+}
+
 #[tauri::command]
 pub fn set_accent_color(state: State<'_, AppState>, color: String) -> Result<(), String> {
     let mut config = state.config.lock().map_err(|e| e.to_string())?;
@@ -354,12 +367,41 @@ pub fn save_custom_theme(state: State<'_, AppState>, theme: crate::types::Custom
 #[tauri::command]
 pub fn delete_custom_theme(state: State<'_, AppState>, id: String) -> Result<(), String> {
     let mut config = state.config.lock().map_err(|e| e.to_string())?;
+    clear_custom_theme_references(&mut config, &id);
+    save_app_config(&config)?;
+    Ok(())
+}
+
+fn clear_custom_theme_references(config: &mut AppConfig, id: &str) {
     config.custom_themes.retain(|t| t.id != id);
     if config.theme == id {
         config.theme = "system".to_string();
     }
-    save_app_config(&config)?;
+    if config.system_light_theme == id {
-    Ok(())
+        config.system_light_theme = "light".to_string();
+    }
+    if config.system_dark_theme == id {
+        config.system_dark_theme = "dark".to_string();
+    }
+}
+
+#[cfg(test)]
+mod custom_theme_reference_tests {
+    use super::*;
+
+    #[test]
+    fn deleting_custom_theme_resets_system_pair_references() {
+        let mut config = AppConfig::default();
+        config.theme = "custom-work".to_string();
+        config.system_light_theme = "custom-work".to_string();
+        config.system_dark_theme = "custom-work".to_string();
+
+        clear_custom_theme_references(&mut config, "custom-work");
+
+        assert_eq!(config.theme, "system");
+        assert_eq!(config.system_light_theme, "light");
+        assert_eq!(config.system_dark_theme, "dark");
+    }
 }
 
 #[tauri::command]

src-tauri/src/lib.rs

@@ -130,6 +130,7 @@ pub fn run() {
             commands::remove_vault,
             commands::get_app_config,
             commands::set_theme,
+            commands::set_system_themes,
             commands::set_accent_color,
             commands::save_custom_theme,
             commands::delete_custom_theme,

src-tauri/src/types.rs

@@ -114,6 +114,12 @@ pub struct AppConfig {
     #[serde(default)]
     pub active_bookmark_id: Option<String>,
     pub theme: String,
+    /// Themes used when `theme` is "system": the frontend picks one by the OS color scheme.
+    /// Default to the plain "light"/"dark" schemes so existing configs keep their behavior.
+    #[serde(default = "default_system_light_theme")]
+    pub system_light_theme: String,
+    #[serde(default = "default_system_dark_theme")]
+    pub system_dark_theme: String,
     #[serde(default)]
     pub accent_color: Option<String>,
     #[serde(default)]
@@ -269,6 +275,14 @@ fn default_ai_model() -> String {
     "claude-sonnet-4-6".to_string()
 }
 
+fn default_system_light_theme() -> String {
+    "light".to_string()
+}
+
+fn default_system_dark_theme() -> String {
+    "dark".to_string()
+}
+
 impl Default for AppConfig {
     fn default() -> Self {
         Self {
@@ -276,6 +290,8 @@ impl Default for AppConfig {
             active_vault: None,
             active_bookmark_id: None,
             theme: "system".to_string(),
+            system_light_theme: default_system_light_theme(),
+            system_dark_theme: default_system_dark_theme(),
             accent_color: None,
             font_size: None,
             font_family: None,
@@ -489,7 +505,7 @@ pub struct TaskItem {
 
 #[cfg(test)]
 mod startup_view_tests {
-    use super::StartupView;
+    use super::{AppConfig, StartupView};
 
     #[test]
     fn serializes_supported_startup_views() {
@@ -510,4 +526,17 @@ mod startup_view_tests {
             StartupView::All
         );
     }
+
+    #[test]
+    fn existing_configs_default_system_theme_pair() {
+        let mut value = serde_json::to_value(AppConfig::default()).unwrap();
+        let object = value.as_object_mut().unwrap();
+        object.remove("system_light_theme");
+        object.remove("system_dark_theme");
+
+        let config: AppConfig = serde_json::from_value(value).unwrap();
+
+        assert_eq!(config.system_light_theme, "light");
+        assert_eq!(config.system_dark_theme, "dark");
+    }
 }

src/lib/api.ts

@@ -43,6 +43,10 @@ export async function setTheme(theme: string): Promise<void> {
   return invoke("set_theme", { theme });
 }
 
+export async function setSystemThemes(light: string, dark: string): Promise<void> {
+  return invoke("set_system_themes", { light, dark });
+}
+
 export async function setAccentColor(color: string): Promise<void> {
   return invoke("set_accent_color", { color });
 }

src/lib/components/AppLayout.svelte

@@ -21,6 +21,8 @@
 		showSearch,
 		showCommandPalette,
 		theme,
+		resolvedTheme,
+		customThemes,
 		focusMode,
 		readOnly,
 		activeNote,
@@ -507,7 +509,8 @@
 					createAndFocusNote();
 					return;
 				case 'toggle-theme': {
-					const isDark = $theme === 'dark' || ($theme === 'system' && window.matchMedia('(prefers-color-scheme: dark)').matches);
+					const customTheme = $customThemes.find(theme => theme.id === $resolvedTheme);
+					const isDark = darkThemes.includes($resolvedTheme) || (customTheme?.is_dark ?? false);
 					const next = isDark ? 'light' : 'dark';
 					$theme = next;
 					setTheme(next);
@@ -565,23 +568,6 @@
 		}
 	}
 
-	function applyTheme(t: string) {
-		const namedThemes = ['solarized-light', 'solarized-dark', 'catppuccin', 'nord', 'tokyo-night', 'github-light', 'github-dark', 'dracula', 'blueberry', 'forest-green', 'gruvbox', 'midnight-tide', 'cherry-blossom', 'synthwave', 'ember', 'moonlit', 'light-coffee', 'dark-coffee', 'cotton-candy', 'crimson', 'cloud', 'peach', 'material-dark', 'material-light', 'monokai', 'rose-pine', 'everforest', 'horizon', 'cyberpunk', 'black', 'one-dark'];
-		const root = document.documentElement;
-		root.classList.remove('dark');
-		root.removeAttribute('data-theme');
-		if (namedThemes.includes(t)) {
-			root.setAttribute('data-theme', t);
-			if (darkThemes.includes(t)) root.classList.add('dark');
-		} else if (t === 'dark' || (t === 'system' && window.matchMedia('(prefers-color-scheme: dark)').matches)) {
-			root.classList.add('dark');
-		}
-	}
-
-	$effect(() => {
-		applyTheme($theme);
-	});
-
 	$effect(() => {
 		$collapsedNotebooks;
 		persistState();
@@ -663,12 +649,6 @@
 			prefetchPromise = readNote(lastNotePath).catch(() => null);
 		}
 
-		applyTheme($theme);
-
-		window.matchMedia('(prefers-color-scheme: dark)').addEventListener('change', () => {
-			if ($theme === 'system') applyTheme('system');
-		});
-
 		// Run sidebar and note list refresh in parallel
 		await Promise.all([sidebar?.refresh(), noteList?.refresh()]);
 

src/lib/components/CommandPalette.svelte

@@ -89,7 +89,6 @@
 			action: () => {
 				$theme = 'system';
 				setTheme('system');
-				applyTheme('system');
 				$showCommandPalette = false;
 			}
 		},
@@ -187,7 +186,7 @@
 		if (namedThemes.includes(t)) {
 			root.setAttribute('data-theme', t);
 			if (darkThemes.includes(t)) root.classList.add('dark');
-		} else if (t === 'dark' || (t === 'system' && window.matchMedia('(prefers-color-scheme: dark)').matches)) {
+		} else if (t === 'dark') {
 			root.classList.add('dark');
 		}
 	}

src/lib/components/Editor.svelte

@@ -370,8 +370,6 @@
 
 	// Info panel
 	let showInfo = $state(false);
-	let infoPanelEl = $state<HTMLElement | null>(null);
-	let infoToggleBtnEl = $state<HTMLElement | null>(null);
 	let wordCount = $state(0);
 	let charCount = $state(0);
 	let infoPathCopyState = $state<'idle' | 'copied' | 'error'>('idle');
@@ -4316,21 +4314,6 @@
 		if ($sourceMode) updateCounts();
 	});
 
-	// Auto-close info panel on click outside
-	$effect(() => {
-		if (!showInfo) return;
-		function onInfoClickAway(e: MouseEvent) {
-			if (
-				infoPanelEl && !infoPanelEl.contains(e.target as Node) &&
-				infoToggleBtnEl && !infoToggleBtnEl.contains(e.target as Node)
-			) {
-				showInfo = false;
-			}
-		}
-		document.addEventListener('mousedown', onInfoClickAway);
-		return () => document.removeEventListener('mousedown', onInfoClickAway);
-	});
-
 	// Close in-note search when switching notes
 	let prevSearchPath = '';
 	$effect(() => {
@@ -6142,7 +6125,6 @@
 					</svg>
 				</button>
 				<button
-					bind:this={infoToggleBtnEl}
 					class="icon-btn"
 					class:active={showInfo}
 					onclick={toggleInfo}
@@ -6487,7 +6469,7 @@
 				</div>
 			{/if}
 			{#if showInfo && $activeNote}
-				<div class="info-panel" bind:this={infoPanelEl}>
+				<div class="info-panel">
 					<div class="info-panel-header">
 						<span class="info-panel-title">Note Info</span>
 						<button class="info-close-btn" onclick={() => showInfo = false}>

src/lib/components/NoteWindow.svelte

@@ -8,8 +8,7 @@
 		activeNotePath,
 		editorDirty,
 		readOnly,
-		sourceMode,
+		sourceMode
-		theme
 	} from '$lib/stores/app';
 	import { readNote } from '$lib/api';
 	import { keybindings, matchAction } from '$lib/keybindings';
@@ -17,8 +16,6 @@
 
 	let { notePath }: { notePath: string } = $props();
 
-	import { darkThemes } from '$lib/platform';
-
 	const appWindow = getCurrentWindow();
 	const isMac = navigator.platform.startsWith('Mac');
 	let editor = $state<Editor>(null!);
@@ -36,20 +33,6 @@
 		return () => { unlisten.then(fn => fn()); };
 	});
 
-	$effect(() => {
-		const t = $theme || 'system';
-		const namedThemes = ['solarized-light', 'solarized-dark', 'catppuccin', 'nord', 'tokyo-night', 'github-light', 'github-dark', 'dracula', 'blueberry', 'forest-green', 'gruvbox', 'midnight-tide', 'cherry-blossom', 'synthwave', 'ember', 'moonlit', 'light-coffee', 'dark-coffee', 'cotton-candy', 'crimson', 'cloud', 'peach', 'material-dark', 'material-light', 'monokai', 'rose-pine', 'everforest', 'horizon', 'cyberpunk', 'black', 'one-dark'];
-		const root = document.documentElement;
-		root.classList.remove('dark');
-		root.removeAttribute('data-theme');
-		if (namedThemes.includes(t)) {
-			root.setAttribute('data-theme', t);
-			if (darkThemes.includes(t)) root.classList.add('dark');
-		} else if (t === 'dark' || (t === 'system' && window.matchMedia('(prefers-color-scheme: dark)').matches)) {
-			root.classList.add('dark');
-		}
-	});
-
 	let lastMouseDown = 0;
 	const RESIZE_EDGE = 6;
 

src/lib/components/SettingsPanel.svelte

@@ -1,6 +1,6 @@
 <script lang="ts">
-	import { showSettings, theme, appConfig, activeVaultConfig, updateAvailable as globalUpdateAvailable, updateObj as globalUpdateObj, installType, settingsTab, vaultReady, androidApkUrl, checkForUpdateMobile, notebookSortMode, isManagedInstall, customThemes } from '$lib/stores/app';
+	import { showSettings, theme, resolvedTheme, appConfig, activeVaultConfig, updateAvailable as globalUpdateAvailable, updateObj as globalUpdateObj, installType, settingsTab, vaultReady, androidApkUrl, checkForUpdateMobile, notebookSortMode, isManagedInstall, customThemes } from '$lib/stores/app';
-	import { setTheme, setAccentColor, setFontSize, setFontFamily, setLineHeight, setUiScale, setContentWidth, setGeneralSettings, importObsidian, createBackup, listBackups, restoreBackup, deleteBackup, setBackupSettings, setAiSettings, testAiConnection, setSyncSettings, testSyncConnection, syncNow, getAppConfig, saveCustomTheme, deleteCustomTheme, exportCustomTheme, importCustomThemes } from '$lib/api';
+	import { setTheme, setSystemThemes, setAccentColor, setFontSize, setFontFamily, setLineHeight, setUiScale, setContentWidth, setGeneralSettings, importObsidian, createBackup, listBackups, restoreBackup, deleteBackup, setBackupSettings, setAiSettings, testAiConnection, setSyncSettings, testSyncConnection, syncNow, getAppConfig, saveCustomTheme, deleteCustomTheme, exportCustomTheme, importCustomThemes } from '$lib/api';
 	import { darkThemes, isMobile, isAndroid } from '$lib/platform';
 	import { open as openDialog, save as saveDialog } from '@tauri-apps/plugin-dialog';
 	import { listen } from '@tauri-apps/api/event';
@@ -418,11 +418,12 @@
 	}
 
 	let isThemeDark = $derived(
-		darkThemes.includes($theme) || ($theme === 'system' && window.matchMedia('(prefers-color-scheme: dark)').matches) ||
+		darkThemes.includes($resolvedTheme) ||
-		($theme.startsWith('custom-') && ($customThemes.find(c => c.id === $theme)?.is_dark ?? false))
+		($resolvedTheme.startsWith('custom-') && ($customThemes.find(c => c.id === $resolvedTheme)?.is_dark ?? false))
 	);
 
 	const themePresets = [
+		{ id: 'system', label: 'System', bg: '#ffffff', sidebar: '#1a1b26', accent: '#5b6abf' },
 		{ id: 'light', label: 'Light', bg: '#ffffff', sidebar: '#f8f9fa', accent: '#5b6abf' },
 		{ id: 'dark', label: 'Dark', bg: '#1a1b26', sidebar: '#1f2029', accent: '#89b4fa' },
 		{ id: 'solarized-light', label: 'Solarized Light', bg: '#fdf6e3', sidebar: '#eee8d5', accent: '#268bd2' },
@@ -527,7 +528,45 @@
 	let themeDropdownOpen = $state(false);
 	let accentDropdownOpen = $state(false);
 	let activeCustomTheme = $derived($customThemes.find(c => c.id === $theme) ?? null);
-	let activeThemePreset = $derived(themePresets.find(p => p.id === $theme) ?? themePresets[0]);
+	let activeThemePreset = $derived(
+		themePresets.find(p => p.id === $theme) ?? themePresets.find(p => p.id === 'light')!
+	);
+
+	// Which theme each OS appearance maps to while `theme` is "system". Custom themes are offered
+	// alongside the built-ins so a light/dark pair can be built out of them.
+	let systemLightTheme = $state($appConfig?.system_light_theme ?? 'light');
+	let systemDarkTheme = $state($appConfig?.system_dark_theme ?? 'dark');
+	let systemPairOpen = $state<'light' | 'dark' | null>(null);
+
+	let pairPresets = $derived([
+		...themePresets.filter(p => p.id !== 'system'),
+		...$customThemes.map(ct => ({
+			id: ct.id,
+			label: ct.name,
+			bg: ct.colors.bg_primary,
+			sidebar: ct.colors.bg_secondary,
+			accent: ct.colors.text_primary,
+		})),
+	]);
+
+	let systemPairRows = $derived([
+		{ key: 'light' as const, title: 'Light appearance', selected: systemLightTheme },
+		{ key: 'dark' as const, title: 'Dark appearance', selected: systemDarkTheme },
+	]);
+
+	function selectSystemPairTheme(which: 'light' | 'dark', id: string) {
+		if (which === 'light') systemLightTheme = id;
+		else systemDarkTheme = id;
+		systemPairOpen = null;
+		if ($appConfig) {
+			$appConfig.system_light_theme = systemLightTheme;
+			$appConfig.system_dark_theme = systemDarkTheme;
+			$appConfig = { ...$appConfig };
+		}
+		setSystemThemes(systemLightTheme, systemDarkTheme).catch((e) =>
+			console.error('Failed to save system themes:', e)
+		);
+	}
 	let activeAccentPreset = $derived(accentPresets.find(p => p.name === activeAccent) ?? accentPresets[0]);
 	let isCustomAccent = $derived(activeAccent.startsWith('#'));
 	let activeAccentColor = $derived(
@@ -553,7 +592,7 @@
 	let customThemeImporting = $state(false);
 
 	function openNewCustomThemeEditor() {
-		const isDark = darkThemes.includes($theme) || ($theme === 'system' && window.matchMedia('(prefers-color-scheme: dark)').matches) || $theme.startsWith('custom-') && ($customThemes.find(c => c.id === $theme)?.is_dark ?? false);
+		const isDark = isThemeDark;
 		customThemeEditing = {
 			id: `custom-${Date.now()}`,
 			name: '',
@@ -597,8 +636,8 @@
 		root.removeAttribute('data-theme');
 		for (const v of varsToClear) root.style.removeProperty(v);
 		const namedThemes = ['solarized-light','solarized-dark','catppuccin','nord','tokyo-night','github-light','github-dark','dracula','blueberry','forest-green','gruvbox','midnight-tide','cherry-blossom','synthwave','ember','moonlit','light-coffee','dark-coffee','cotton-candy','crimson','cloud','peach','material-dark','material-light','monokai','rose-pine','everforest','horizon','cyberpunk','black','one-dark'];
-		if ($theme.startsWith('custom-')) {
+		if ($resolvedTheme.startsWith('custom-')) {
-			const ct = $customThemes.find(c => c.id === $theme);
+			const ct = $customThemes.find(c => c.id === $resolvedTheme);
 			if (ct) {
 				root.style.setProperty('--bg-primary', ct.colors.bg_primary);
 				root.style.setProperty('--bg-secondary', ct.colors.bg_secondary);
@@ -613,10 +652,10 @@
 				root.style.setProperty('--text-tertiary', ct.colors.text_secondary);
 				if (ct.is_dark) root.classList.add('dark');
 			}
-		} else if (namedThemes.includes($theme)) {
+		} else if (namedThemes.includes($resolvedTheme)) {
-			root.setAttribute('data-theme', $theme);
+			root.setAttribute('data-theme', $resolvedTheme);
-			if (darkThemes.includes($theme)) root.classList.add('dark');
+			if (darkThemes.includes($resolvedTheme)) root.classList.add('dark');
-		} else if ($theme === 'dark' || ($theme === 'system' && window.matchMedia('(prefers-color-scheme: dark)').matches)) {
+		} else if ($resolvedTheme === 'dark') {
 			root.classList.add('dark');
 		}
 	}
@@ -651,9 +690,15 @@
 	async function removeCustomTheme(ct: CustomTheme) {
 		try {
 			await deleteCustomTheme(ct.id);
+			if (systemLightTheme === ct.id) systemLightTheme = 'light';
+			if (systemDarkTheme === ct.id) systemDarkTheme = 'dark';
 			if ($appConfig) {
-				$appConfig.custom_themes = $appConfig.custom_themes.filter(t => t.id !== ct.id);
+				$appConfig = {
-				$appConfig = { ...$appConfig };
+					...$appConfig,
+					custom_themes: $appConfig.custom_themes.filter(t => t.id !== ct.id),
+					system_light_theme: systemLightTheme,
+					system_dark_theme: systemDarkTheme,
+				};
 			}
 			if ($theme === ct.id) {
 				$theme = 'system';
@@ -816,7 +861,9 @@
 		$theme = preset.id;
 		setTheme(preset.id);
 		themeDropdownOpen = false;
-		selectCustomAccent(preset.accent);
+		// "System" has no palette of its own, it defers to whichever paired theme is active, so it
+		// must not overwrite the accent the way a concrete theme does.
+		if (preset.id !== 'system') selectCustomAccent(preset.accent);
 	}
 
 	function selectAccent(preset: typeof accentPresets[0]) {
@@ -827,7 +874,7 @@
 
 	function applyAccent(preset: typeof accentPresets[0]) {
 		const root = document.documentElement;
-		const isDark = darkThemes.includes($theme) || ($theme === 'system' && window.matchMedia('(prefers-color-scheme: dark)').matches);
+		const isDark = isThemeDark;
 		const color = isDark ? preset.dark : preset.light;
 
 		root.style.setProperty('--accent', color);
@@ -850,7 +897,7 @@
 
 	function applyCustomAccent(hex: string) {
 		const root = document.documentElement;
-		const isDark = darkThemes.includes($theme) || ($theme === 'system' && window.matchMedia('(prefers-color-scheme: dark)').matches);
+		const isDark = isThemeDark;
 		root.style.setProperty('--accent', hex);
 		root.style.setProperty('--text-accent', hex);
 		root.style.setProperty('--accent-hover', hex);
@@ -1003,9 +1050,9 @@
 		}
 	});
 
-	// Re-apply when theme changes
+	// Re-apply when the concrete theme changes, including an OS appearance switch.
 	$effect(() => {
-		const _ = $theme;
+		const _ = $resolvedTheme;
 		const preset = accentPresets.find(p => p.name === activeAccent);
 		if (preset) {
 			applyAccent(preset);
@@ -1419,6 +1466,9 @@
 										</div>
 									{/if}
 								</div>
+								{#if $theme === 'system'}
+									<span class="setting-hint">Follows the operating system appearance.</span>
+								{/if}
 							</div>
 
 							<div class="settings-section">
@@ -1467,6 +1517,54 @@
 									{/if}
 								</div>
 							</div>
+
+							{#if $theme === 'system'}
+								{#each systemPairRows as row}
+									<div class="settings-section">
+										<h3>{row.title}</h3>
+										<div class="dropdown-wrap">
+											<button
+												class="dropdown-trigger"
+												class:open={systemPairOpen === row.key}
+												onclick={() => { systemPairOpen = systemPairOpen === row.key ? null : row.key; themeDropdownOpen = false; accentDropdownOpen = false; }}
+											>
+												{#each pairPresets.filter(p => p.id === row.selected) as preset}
+													<span class="dropdown-preview" style="--preview-bg: {preset.bg}; --preview-sidebar: {preset.sidebar}; --preview-accent: {preset.accent}">
+														<span class="preview-sidebar"></span>
+														<span class="preview-main">
+															<span class="preview-accent-bar"></span>
+														</span>
+													</span>
+													<span class="dropdown-trigger-label">{preset.label}</span>
+												{/each}
+												<svg class="dropdown-chevron" viewBox="0 0 16 16" fill="none"><path d="M4 6l4 4 4-4" stroke="currentColor" stroke-width="1.5" stroke-linecap="round" stroke-linejoin="round"/></svg>
+											</button>
+											{#if systemPairOpen === row.key}
+												<div class="dropdown-list" use:clickOutside={() => systemPairOpen = null}>
+													{#each pairPresets as preset}
+														<button
+															class="dropdown-item"
+															class:active={row.selected === preset.id}
+															onclick={() => selectSystemPairTheme(row.key, preset.id)}
+														>
+															<span class="dropdown-preview" style="--preview-bg: {preset.bg}; --preview-sidebar: {preset.sidebar}; --preview-accent: {preset.accent}">
+																<span class="preview-sidebar"></span>
+																<span class="preview-main">
+																	<span class="preview-accent-bar"></span>
+																</span>
+															</span>
+															<span class="dropdown-item-label">{preset.label}</span>
+															{#if row.selected === preset.id}
+																<svg class="dropdown-check" viewBox="0 0 16 16" fill="none"><path d="M3 8l4 4 6-6" stroke="currentColor" stroke-width="1.5" stroke-linecap="round" stroke-linejoin="round"/></svg>
+															{/if}
+														</button>
+													{/each}
+												</div>
+											{/if}
+										</div>
+									</div>
+								{/each}
+							{/if}
 							</div>
 
 							<!-- Custom Themes -->

src/lib/stores/app.ts

@@ -89,6 +89,29 @@ export const readOnly = writable(false);
 export const theme = writable<string>("system");
 export const customThemes = derived(appConfig, ($c): CustomTheme[] => $c?.custom_themes ?? []);
 
+// Whether the OS is currently in dark mode. Held in a store (rather than read at each call site)
+// so the theme re-resolves when the user flips appearance while the app is open.
+const darkQuery =
+  typeof window !== "undefined" ? window.matchMedia("(prefers-color-scheme: dark)") : null;
+export const systemPrefersDark = writable<boolean>(darkQuery?.matches ?? false);
+darkQuery?.addEventListener("change", (e) => systemPrefersDark.set(e.matches));
+
+// The theme to actually render: "system" resolves to the configured light/dark pair, everything
+// else passes through. Falls back to the plain schemes when no pair is configured yet.
+export const resolvedTheme = derived(
+  [theme, appConfig, systemPrefersDark],
+  ([$theme, $config, $prefersDark]): string => {
+    if ($theme !== "system") return $theme;
+    const fallback = $prefersDark ? "dark" : "light";
+    const paired = $prefersDark ? $config?.system_dark_theme : $config?.system_light_theme;
+    if (!paired) return fallback;
+    if (paired.startsWith("custom-") && !$config?.custom_themes.some((item) => item.id === paired)) {
+      return fallback;
+    }
+    return paired;
+  },
+);
+
 // Sync (WebDAV) - global status so the top-bar button reflects any sync,
 // whoever triggered it (manual button, settings, interval, on-change).
 export const syncState = writable<{ running: boolean; error: string | null }>({

src/lib/types.ts

@@ -88,6 +88,8 @@ export interface AppConfig {
   active_vault: string | null;
   active_bookmark_id?: string | null;
   theme: string;
+  system_light_theme: string;
+  system_dark_theme: string;
   accent_color: string | null;
   font_size: number | null;
   font_family: string | null;

src/routes/+layout.svelte

@@ -1,7 +1,7 @@
 <script lang="ts">
 	import { onMount } from 'svelte';
 	import '../app.css';
-	import { theme, appConfig, activeNote, activeNotePath, installType, platformIsMobile, checkForUpdate, checkForUpdateMobile, isManagedInstall, customThemes } from '$lib/stores/app';
+	import { resolvedTheme, appConfig, activeNote, activeNotePath, installType, platformIsMobile, checkForUpdate, checkForUpdateMobile, isManagedInstall, customThemes } from '$lib/stores/app';
 	import { openFile, openUrl, readNote, getInstallType, isMobilePlatform } from '$lib/api';
 	import { get } from 'svelte/store';
 	import { darkThemes, isMobile, isAndroid } from '$lib/platform';
@@ -10,9 +10,11 @@
 
 	let { children } = $props();
 
-	// Reactively apply theme class to <html> whenever $theme or custom themes change
+	// Reactively apply theme class to <html> whenever the resolved theme or custom themes change.
+	// $resolvedTheme already maps "system" onto the configured light/dark pair, so flipping the OS
+	// appearance re-runs this effect.
 	$effect(() => {
-		applyTheme($theme, $customThemes);
+		applyTheme($resolvedTheme, $customThemes);
 	});
 
 	// Apply link arrow visibility from config

src/routes/+page.svelte

@@ -155,8 +155,13 @@
 			});
 			$theme = config.theme || 'system';
 
-			// Apply theme immediately to prevent flash
+			// Apply theme immediately to prevent flash. Runs before the stores settle, so resolve
-			const themeValue = config.theme || 'system';
+			// "system" against the configured pair here the same way resolvedTheme does.
+			const prefersDark = window.matchMedia('(prefers-color-scheme: dark)').matches;
+			const rawTheme = config.theme || 'system';
+			const themeValue = rawTheme === 'system'
+				? (prefersDark ? config.system_dark_theme || 'dark' : config.system_light_theme || 'light')
+				: rawTheme;
 			const root = document.documentElement;
 			const namedThemes = ['solarized-light', 'solarized-dark', 'catppuccin', 'nord', 'tokyo-night', 'github-light', 'github-dark', 'dracula', 'blueberry', 'forest-green', 'gruvbox', 'midnight-tide', 'cherry-blossom', 'synthwave', 'ember', 'moonlit', 'light-coffee', 'dark-coffee', 'cotton-candy', 'crimson', 'cloud', 'peach', 'material-dark', 'material-light', 'monokai', 'rose-pine', 'everforest', 'horizon', 'cyberpunk', 'black', 'one-dark'];
 			root.classList.remove('dark');
@@ -164,7 +169,7 @@
 			if (namedThemes.includes(themeValue)) {
 				root.setAttribute('data-theme', themeValue);
 				if (darkThemes.includes(themeValue)) root.classList.add('dark');
-			} else if (themeValue === 'dark' || (themeValue === 'system' && window.matchMedia('(prefers-color-scheme: dark)').matches)) {
+			} else if (themeValue === 'dark') {
 				root.classList.add('dark');
 			}
 
@@ -192,8 +197,8 @@
 			}
 			// Apply saved accent
 			if (config.accent_color) {
-				const themeVal = config.theme || 'light';
+				const customTheme = config.custom_themes.find(theme => theme.id === themeValue);
-				const isDark = darkThemes.includes(themeVal) || (themeVal === 'system' && window.matchMedia('(prefers-color-scheme: dark)').matches);
+				const isDark = darkThemes.includes(themeValue) || (customTheme?.is_dark ?? false);
 				let color: string | null = null;
 				if (config.accent_color.startsWith('#')) {
 					color = config.accent_color;