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You could try a relational database (like FileMaker, although that's not free), a mind map (I've never used one, so I don't know what features they have), or some kind of wiki. I use Scrivener with...
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#4: Attribution notice removed
Source: https://writers.stackexchange.com/a/19200 License name: CC BY-SA 3.0 License URL: https://creativecommons.org/licenses/by-sa/3.0/
#3: Attribution notice added
Source: https://writers.stackexchange.com/a/19200 License name: CC BY-SA 3.0 License URL: https://creativecommons.org/licenses/by-sa/3.0/