feat(core): linked doc visiblity setting and new sidebar layout (#12836)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Added a setting to control the visibility of linked document
structures in the sidebar, enabled by default.
- Introduced a "dense" mode for workspace selectors and cards, providing
a more compact display.

- **Improvements**
- Refined sidebar and navigation panel layouts with updated padding,
spacing, and avatar/button sizing for a cleaner and more consistent
appearance.
- Enhanced sidebar appearance settings UI, including new localization
for the linked doc visibility option.
- Updated color theming and spacing in sidebar menu items and quick
search input for better usability.
- Enabled collapsible behavior control for navigation panel tree nodes,
improving user interaction flexibility.

- **Style**
- Adjusted various component styles for improved compactness and
alignment across the sidebar and navigation panels.
- Reduced sizes and padding of buttons and icons for a tidier interface.
- Updated CSS variables and dynamic sizing for workspace cards to
support dense mode.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

packages/common/infra/src/atom/settings.ts

@@ -16,6 +16,7 @@ export type AppSetting = {
   autoCheckUpdate: boolean;
   autoDownloadUpdate: boolean;
   enableTelemetry: boolean;
+  showLinkedDocInSidebar: boolean;
 };
 export const windowFrameStyleOptions: AppSetting['windowFrameStyle'][] = [
   'frameless',
@@ -33,6 +34,7 @@ const appSettingBaseAtom = atomWithStorage<AppSetting>(
     autoCheckUpdate: true,
     autoDownloadUpdate: true,
     enableTelemetry: true,
+    showLinkedDocInSidebar: true,
   },
   undefined,
   {