bicycle VS outshine

I finally found a way to organize my huge init.el. Outline-minor-mode, together with https://github.com/tarsius/bicycle and https://github.com/tarsius/outline-minor-faces/, make the following nice view.

The bicycle package makes things a little easier to manage/bind.

I'm certainly sympathetic to these kinds of problems. I agree with @plantarum that you seem to be doing what needs to be done though. But one further thing might be to search for simpler package implementations of what you need. For example, I used to use Outshine but now use bicycle and outline-minor-faces, which do everything I wanted Outshine to do without any of the headaches. They might be worth a look.

Note that outshine also supports editing of comment-blocks-as-org-syntax (via outorg) and many other legacy features.

I use https://github.com/alphapapa/outshine for this.

Some further digging in the Outshine github issues list shed more light on the problem, and suggested modifying the advice function for org-store-log-note in outshine.el. Since 1) I'm not keen on modifying packages (I might end up breaking something else), and 2) I only used Outshine (version 3.1.pre) for smart navigation and code collapsing, I figured a simpler solution would be to just remove the advice from org-store-log-note in my init.el after everything was loaded.

I've found that outshine is good enough for me to avoid the need for a literate config. I don't see it discussed often and I wonder why.