Some thoughts.
I would prefer breakpoints to be disctinct from the current execution position.
When thinking analogously to a debugger, Breakpoints indicate where the program should stop not where the program currently is, and consequently breakpoints can exist on multiple lines at once.
I prefer a different graphic to indicate the active line. A line highlighted colour would be enough
On my machine the area that is active for the 'line annotations' pop-up menu has no visual cue to say that it is there.
It appears to crete a new 'line annotations' menu for each hover with the old menu lingering a short time before dissapearing, this looks quite odd.
I have achieved multiple perminantly open 'line annotations' menus at the same time.
It would be beneficial to have line ranges on annotations so you can higlight a block of code.
Adding a new frame duplicating the current annotations would be good. Either that or have a way to declare the same annotation applies to multiple frames.
Having the ability for an annotation to collapse a section of code to ... for within a single line or \n...\n for multi line collapse would let people focus on the code being explained.
It definitely needs a more visible way to lead your focus. It's hard to tell what you're supposed to be looking at.
One bit of UX feedback - the modal with the commentary text is a bit low on the screen (at least on chrome on a 15 inch retina display), I think it would be better to have it higher up on the page, or possibly even aligned with the current line?
a related project you might be interested in https://ourcodestories.com/