Organising research for a thesis or dissertation with a web highlighter

A structure that survives three years: one workspace per chapter, tags for arguments, highlights that keep their source, and a bibliography you export at the end.

Set up once

Projects by chapter. In Vite Research a project is a workspace with folders and notes. Three projects are free; Pro removes the limit. Thoughts (quick captures) and Knowledge (reference notes) exist from the start.
Tags by argument, not by topic. Tags such as supports-h1, counter-evidence, method, definition let you pull every passage that serves one claim; topic tags duplicate what your chapters already do.
Feeds for the literature. Add the 10 to 20 journals of your field from the field pages and the preprint category, and skim them weekly.

While reading

Highlight the sentence you would quote, not the paragraph. Write the comment as the note you will want in a year: why it matters, what it contradicts. Save the page to the Library when you will cite it; the snapshot means the source is still there at submission.

While writing

The notes editor embeds saved highlights and articles into a note, links notes with [[wiki-links]], supports headings, lists, task lists, code, KaTeX formulas and Mermaid diagrams, and exports Markdown. The Cite dialog gives APA 7, MLA 9 or Chicago per source; the bibliography export produces a .bib file for LaTeX or your reference manager.

What to keep elsewhere

PDF annotation and long-form writing with a word processor plugin belong to Zotero, Mendeley or your editor; Vite Research holds the web layer: the pages, the passages, the sources and the feeds.