So, awhile ago, @aartaka approached me and asked a series of Nyxt-related questions for some project of his. He asked me if I could post my answe to the last question, which was ideas for improvement on Nyxt. So, without further ado:
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More rich support for metadata, especially WebAnnotation-style annotation storage as well as hierarchical tagging/ontological controlled vocabularies,
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Better, more multi-faceted search,
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Hybrid data formats, one human-readable and ideally S-exp-based, the other binary, full-text indexed, and FAST, with the ability to move entries between the two (or more),
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Interconnections between entries are ideally a graph or a hypergraph, with an appropriate eDSL for OpenCog/Atomspace-style (hyper)graph searching, and finally,
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mnemonic sets of keybindings for all this.