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If all you have is just an idea my recommendation is to make this idea more concrete. What are the requirements your software has? Write them all down. If you have a lot of requirements mark the important ones. Now you want to think about architecture: how should your implementation be structured? What parts should exist, and what are the interfaces in ...
From your requirements above, it would seem that Trello may be a good solution to your preferred organization system. A single Trello 'board' contains a system of 'lists' which can contain unlimited 'cards'. Each card can contain a variety of content including tags, links, files, etc. And Trello can very easily be setup for GTD use.
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