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/chat/view/subcomponents/ChatComposer.tsx

@@ -197,7 +197,7 @@ export default function ChatComposer({
   const hasPendingPermissions = pendingPermissionRequests.length > 0;
 
   return (
-    <div className="chat-composer-shell flex-shrink-0 p-2 pb-2 sm:p-4 sm:pb-4 md:p-4 md:pb-6">
+    <div className="chat-composer-shell flex-shrink-0 px-2 pb-2 pt-0 sm:px-4 sm:pb-4 md:px-4 md:pb-6">
       {!hasPendingPermissions && (
         <ActivityIndicator activity={activity} onAbort={onAbortSession} />
       )}