Hmm.. I kind of get what you're saying.. but there is nothing to tread on. I left-click and the red diamond shows up which indicates a break point is set. It's not registering as a bookmark, as I've tested it by left-clicking in a few areas and then [using CTRL+. to cycle through](https://github.com/geany/geany/blob/master/doc/geany.txt#bookmarks), but nothing happens. If I use CTRL+m to set a bookmark, I can navigate through them using CTRL+..
Basically it seems the debugger plug-in is just taking precedence over the bookmark feature.