Good feedback. Thank you! This iteration explores my question that while navigation history is a tree, what do people want on the screen at the same time? Personally, I find myself usually wanting 2-3 units of information on the screen (most often, a caller and callee). That's why panes are draggable from one column to another. The navigation is semantic but the panes are unopinionated.

Iteration 01 https://artifacts.bypaulshen.com/code-explorer/01/?snapshot=... implements exactly what you suggest with showing connections. Closing a pane will recursively close children. Also references are tied to the pane (point 4)

5. yes! I'm going through iterations of exploration but will consider these important points when/if productionizing.