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Based on our record, VOoM should be more popular than Manuskript. It has been mentiond 2 times since March 2021. We are tracking product recommendations and mentions on various public social media platforms and blogs. They can help you identify which product is more popular and what people think of it.
Looks like you want something that integrates well with your workflow. The closest to your description seems to be Manuskript although I haven't used it. But your requirement of "keeping notes and frameworks and linking back and forth" should be possible by stitching together existing Linux tools using a syntax like markdown or asciidoc so that you can use any text editor to write your story and use external tools... Source: about 4 years ago
I write notes in plain markdown and use VOoM (Vim Outliner of Markups) to help navigate & manage sections. Not the trendiest plugin but it's super stable, supports a wide range of markup formats (markdown, wiki, vimwiki, org, fmr, latex, asciidoc, etc.), and has intuitive keybindings. Combine with your favorite search plugin (ack, ag, vimgrep) and you're off. Source: over 3 years ago
I use both voom and tagbar for this. Voom provides some basic outlining features and supports markdown out of the box. Tagbar is a general tag-viewer (see its wiki for improving markdown navigation: https://github.com/preservim/tagbar/wiki#markdown). Source: about 4 years ago
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