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Check out org-mode. Handles todos, scheduling tasks, timers, you can link directly to a file or an email (not a copy, but a link emacs follows into your mail reader, such as mu4e/gnus/wanderlust, for that specific email). It will auto generate an agenda from multiple todo files spread across your filesystem.

http://orgmode.org/worg/org-tutorials/orgtutorial_dto.html

There are some mobile apps but I've never used them.

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org-mode is great and I use it to write longer, unorganized sorts of things. It was amazing to have a place I could keep track of my time to the minute, extend if I wanted to do basically anything, etc. I missed the visualized nature, however, as I found the visual feedback to be imperative to my taste.

calfw can integrate with org. I mostly use the integration as a way point for gcal sync, but even if the integration isn't exactly what you want, adding a new source to calfw is very easy

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