[__d]

I use a basic Markdown document, with a bullet-point list of "todo" items.

For things that need further breakdown, I use indented sub-items to decompose features into achievable chunks.

I then use strikethrough formatting to mark things as done. On GitHub this is done with tilde characters; other (proper) Markdown parsers might need to use <del>.

I find it usually means a 1-page overview of the initial scope of the project, which helps me refine the concept as well as the todo list.

Once the initial work is done, I tend to use GitHub issues. That might not be until I've done a few iterations of the Markdown doc though.