Fix scratchbook window z-index stacking and improve styling

[dannon]

Fix scratchbook window z-index stacking, iframe click-to-front, and improve styling.

• Stop passing index to every WinBox.new() call — WinBox's constructor calls focus() which auto-increments z-index, but then the index parameter overwrites it. Pass it only on the first window to set a z-index floor above Galaxy UI.
• Add a transparent click overlay on unfocused windows so clicking iframe content brings the window to front. WinBox's mousedown-based focus can't detect clicks inside iframes. The overlay uses pointer-events:none on the focused window so the iframe works normally.
• Style windows to match Galaxy UI — brand-primary title bar, Bootstrap modal shadow, Galaxy font family, proper body background. Shadow and border removed when maximized.

Addresses feedback from @nekrut

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. Enable Window Manager (grid icon in masthead)
  2. Open multiple dataset visualizations — each new window should appear on top
  3. Click inside a background window's content — it should come to front
  4. Verify styling: shadow, Galaxy font, dark blue title bar
  5. Maximize a window — shadow/border should disappear

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[guerler]

Some of the newly opened windows remain behind already existing ones, and the last one does not come to the front even when clicked on. The workaround right now is to select another window first and then reselect the last window.

[dannon]

Thanks for the screencast! There were actually two separate issues here:

1. Z-index stacking — WinBox's constructor calls focus() (which auto-increments z-index) and then the index parameter immediately overwrites it back to the passed value. Since we were passing index: 850 to every window, they all ended up at the same z-index. Fixed by only passing index on the first window to establish a floor, then letting WinBox auto-manage from there.

2. Click-to-front not working through iframes — This is a pre-existing issue, not introduced by this PR. WinBox's focus management relies on mousedown events, which don't propagate out of iframes. But since we're in here anyway, added a fix: a transparent overlay on unfocused windows captures clicks and brings the window to front, then gets out of the way (via pointer-events: none) so the iframe content works normally.

[guerler]

Works very well! Thank you.

[github-actions]

This PR was merged without a "kind/" label, please correct.