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/code-editor/view/subcomponents/markdown/MarkdownPreview.tsx

@@ -12,6 +12,9 @@ type MarkdownPreviewProps = {
 
 const markdownPreviewComponents: Components = {
   code: MarkdownCodeBlock,
+  // MarkdownCodeBlock renders its own highlighted <pre>; passthrough prevents a
+  // second Typography-styled <pre> shell from framing it.
+  pre: ({ children }) => <>{children}</>,
   blockquote: ({ children }) => (
     <blockquote className="my-2 border-l-4 border-gray-300 pl-4 italic text-gray-600 dark:border-gray-600 dark:text-gray-400">
       {children}