I find it hard to pickup right where I left off after a week or more if the project is already complex, with or without notes.
I tried to use something that works like charts, forget the name, but didn’t use it much, it felt like too much work to do.
I used Trello for a time, worked well, I just didn’t stick to it. This might be more of a discipline issue on my part.
What I feel works best for me is a big drawing board (or two) with chalk and posted notes.
I’ve been able to keep track better and design with drawing apps, but I really need a big screen device to take advantage of it.
I still use CherryTree, I just don’t like the formatting, but it’s really good for organizing and can do linking between sections and subsections.
I’m developing software for 20 years now … never worked in a team which is good and bad, but that being said … I never used visual source safe, GitHub, or anything else.
I’m using a very primal and stupid method, which is keeping each project in organized folders, and I use notepad to write any kind of notes related to this project.
But i always try to write meaningful comments inside my code specially when the code looks weird
I know this is not much of a help, but this is to let you know that you are not alone
Personally, I prefer drafting an initial game design document on paper. Then I rewrite it to an online document, or to a document in some file sharing system like Dropbox or GitHub.
Finally, I create a Kanban board to GitHub projects based on the design document and start working on it. That way I can see what components are (still) needed and how the project is progressing.
I take notes(use an app, paper whatever is best for you), use Trello and leave myself some notes through comments on what I plan to do next and warn my future self if I’m leaving something incomplete. Doing it all saves me significant time when I try to get back on track.