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Tree - Write documents in tree-like organisation with Markdown
Nifty - Manage projects, work, and communications in one place.
NotePlan - Make plans inside an individual markdown note for every day in your calendar. Use it as a journal for your daily tasks and plan todos in advance. For Mac, iPhone and iPad.
Trello - Infinitely flexible. Incredibly easy to use. Great mobile apps. It's free. Trello keeps track of everything, from the big picture to the minute details.
Markdown New Tab - Write notes in Markdown directly in the 'New Tab' page
Jira - The #1 software development tool used by agile teams. Jira Software is built for every member of your software team to plan, track, and release great software.