I just rendered and previewed everything locally. I really like the proposed changes; it feels like a clear improvement on top of what we already have.

I'm tempted to merge as-is, but two very minor thoughts first:

• While the highlighted "pink" colour looks good against the white background, it's a little garish for my tastes against the teal background. Is there perhaps a softer option that we could try? This is not a strongly held opinion, and you're the color expert, so feel free to go with your preferred aesthetic.
• One collateral benefit of moving everything to the navbar is that we "recover" a menu level. Along those lines, I can see that you already added a "Main functions" entry in the References section and I like this idea. Similarly, I wonder whether it makes sense to create a "Types" (or "Plot types") menu entry where can nest "Shapes", "Visualizations", and co. under? (Note: This is what we had originally, but we dropped it to avoid too-deep menu nesting... which may be moot now that the navbar has given us one menu level back.)