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I use a TODO.md doc in the project root as long as it's <50 lines of todos and issues. You can use `- [ ]` to create checkbox lists in markdown.

For a larger project I use GitHub issues with tags.

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This is a similar method to what I use as well.

I even wrote a Vim syntax plugin for the todo files: https://github.com/tomswartz07/vim-todo

Markdown is perfect for to-do lists, I keep 5 days (1 week) of todo files that I compile to HTML and view on any device in-browser, and edit on whatever machine I'm working from at the time.

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