style(ui): rework light/dark theme to make it visually consistent

Rework the color system around warm neutrals and route hardcoded
surfaces through theme tokens for consistency.

- Theme tokens (index.css, ThemeContext): warm cream light mode and
  neutral charcoal dark mode, replacing the pure-white/blue-tinted
  palette; update PWA theme-color meta
- Code blocks: soft grey background in light mode via
  oneLight/oneDark, and drop the Tailwind Typography <pre> shell that
  framed the highlighter in a dark box
- Dropdowns/panels: convert CommandMenu, Quick Settings, and the JSON
  response block from hardcoded gray/slate to popover/muted/border
  tokens
- Git panel: Publish button purple -> primary blue
- Composer: drop top padding so the input sits flush with the thread

src/components/quick-settings-panel/view/QuickSettingsSection.tsx

@@ -13,7 +13,7 @@ export default function QuickSettingsSection({
 }: QuickSettingsSectionProps) {
   return (
     <div className={`space-y-2 ${className}`}>
-      <h4 className="mb-2 text-xs font-semibold uppercase tracking-wider text-gray-500 dark:text-gray-400">
+      <h4 className="mb-2 text-xs font-semibold uppercase tracking-wider text-muted-foreground">
         {title}
       </h4>
       {children}