Thesys is a research workspace where you search academic papers, build your own library, and ask questions that answer with citations you can click straight onto the highlighted passage of the PDF. Discovery searches OpenAlex and arXiv in one pool, so a paper you find can be previewed and added to your library without leaving the workspace. Uploaded PDFs are ingested locally, and when you ask a question the answer cites its sources in the document, jumping the preview to the retrieved passage with either a full-passage or a tighter focused highlight. Reader mode opens a paper full-width so you can select any span of text and ask about that exact passage. Document summaries follow a consistent structure of problem statement, methodology, key findings, limitations, and metrics, with citations that still land on the source text. Figures and flowcharts are described during ingest, so questions and summaries can reference them too. When two papers disagree, Compare mode takes one claim and classifies each retrieved pair as corroboratory, contradictory, or neutral, with confidence shown in a side panel. Your bibliography exports as BibTeX, RIS, EndNote, or CSV for whatever reference manager you already use. Papers, embeddings, and chat history stay on your own disk the whole time. Running on a dedicated VPS on RepoCloud with guaranteed CPU, RAM, and SSD, full root SSH access, and a browser serial console. AGPL-3.0 licensed.