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I'm willing to bet Scrivener can handle a lot of what you're looking for. I will cheerfully admit I haven't even read the documentation (I'm a Mac user... we don'need no steenken manuals) so it's g...
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Source: https://writers.stackexchange.com/a/6124 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/6124 License name: CC BY-SA 3.0 License URL: https://creativecommons.org/licenses/by-sa/3.0/
#2: Initial revision
I'm willing to bet [Scrivener](http://literatureandlatte.com/) can handle a lot of what you're looking for. I will cheerfully admit I haven't even read the documentation (I'm a Mac user... we don'need no steenken manuals) so it's got powerful tools I don't even know much about. You can separate your work into individual documents (section, subsection) which can then be put into folders and dragged around on a virtual corkboard, and compiled into a single document for reading over. You can add keywords, highlight chunks of text in multiple colors, create internal hyperlinks, and do word counts and word frequency counts. I have no idea what "visualization of flow" means, so I can't advise you there. You can download it and try it for free for a month, and export everything to Word or text so it's not held proprietarily hostage.