Read papers in DSH: read, ask and take notes in one place

Quick start · Highlights · TODO · Developer handbook · 简体中文

[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](./LICENSE) [![DSH Plugin](https://img.shields.io/badge/DSH-plugin-4f46e5)](https://github.com/topics/dsh-plugin) [![DSH](https://img.shields.io/badge/DSH-0.1.7%2B-6366f1)](https://github.com/deepseek-ai/deepseek-harness) [![Repo](https://img.shields.io/badge/github-PhysicalAI--0%2Fdsh--paperforge-181717?logo=github)](https://github.com/PhysicalAI-0/dsh-paperforge)

**Understand the paper. Keep your own thinking.** Open a PDF from the paper library to bring the paper, its dedicated AI session and your Markdown notes side by side. Select a difficult passage to ask AI with the context included; highlight key text or capture a figure, and your highlights and screenshots go straight into local notes. Come back to the paper and pick up where your thinking left off. ##

News - **2026-09-29** - Native multi-column reading layout: session list on the left, the paper's AI session in the middle, PDF｜notes on the right. - Added session Summary and Copy path; notes now live in `paperforge_notes`, and images no longer referenced by any note are cleaned up. - Block-level Markdown editing: every `.md` is editable in place, with autosave. - Reading flow rebuilt: paper library, live notes preview, one dedicated AI session per paper. - **2026-09-28** — First release; installs through DSH's native `dsh plugin` command. ##

Highlights ![Reading layout: session list on the left, the paper's AI session in the middle, PDF and notes on the right](docs/images/en/reading.png)

Paper library Papers in the left sidebar lists the PDFs in your workspace; pick one to open the reading layout	Annotate Highlights (six colours) and region screenshots are saved to your notes automatically; selections can also be copied as plain text or Markdown quotes	Ask AI Ask AI on a selection or AI in the PDF header opens the paper's session; questions about a selection include `@paper`, the page number and the passage
Markdown editing Every `.md` is editable in place: click a block to edit its source, leave to render it; autosaves and merges with changes from the plugin or the AI	Summary Tick sessions on the library's Sessions tab to produce one Summary in Markdown: referenced three at a time, then combined	Copy path The copy icon in any document header copies the file's path in one click

Click a block to edit its source; the rest stays rendered

_{Notes: click any block to edit its source}

Summary: the AI writes a summary of several sessions into Markdown

_{Summary: the AI combines the ticked sessions into one Markdown file}

_{Paper pages in the screenshots are from Vaswani et al., Attention Is All You Need (arXiv:1706.03762), reproduced with attribution for scholarly use as Google permits. The logo and section icons were generated with an AI image model.} ##

Quick start Requirements: DSH `0.1.7+` and `pnpm` on your PATH. ```bash dsh plugin --profile web add github:PhysicalAI-0/dsh-paperforge # or install from a local clone (code changes take effect after restarting dsh web): git clone https://github.com/PhysicalAI-0/dsh-paperforge.git && cd dsh-paperforge dsh plugin --profile web add . ``` Start `dsh web` in the folder that holds your papers (that folder must also be a DSH workspace). A **Papers** entry in the left sidebar means it's installed. Uninstall: `dsh plugin --profile web remove dsh-paperforge`. ##

Where notes go ```text /paperforge_notes/ ├─ /.md notes (standard Markdown, editable in place) ├─ /assets/ captures; images not referenced by any note are removed after about 2 minutes ├─ /highlights.json, session.json highlight positions, link to the paper's session └─ Summary/ session summaries ``` ##

Configuration (optional) Override by id in `~/.dsh/profiles/web/cordis.patch.yml`: ```yaml - id: paperforge config: workspaceRoot: # defaults to the folder dsh web starts in notesDir: paperforge_notes # notes root folder (older versions used notes) model: # model for paper sessions; omit to keep your current model provider: deepseek-official name: deepseek-flash reasoningEffort: high ``` Don't use `- insert:` (the plugin would load twice). When `model` is set, DSH also saves it as the default model for new sessions. ##

TODO - [ ] Instant-rendering Markdown (Vditor-style): click an image to zoom, drag blocks to reorder - [ ] Rich rendering: mermaid flowcharts / sequence diagrams / Gantt charts, echarts, mind maps - [ ] Several sessions for the same paper (the **AI** header button) - [ ] Tools and a skill for reading papers by page and by figure, cutting the token cost of reading figures - [ ] Write key Q&A points back into the notes automatically - [ ] Pure JavaScript: replace the Python sidecar with `mupdf`; make the library scan asynchronous ##

Known limitations - The right sidebar has at most two panes (a DSH limit); float extra windows out. - Before its first question, a paper session shows as "New session" in the left list, and DSH's "New session" may reuse it. - Markdown is edited block by block: undo covers only the current block; reference-style links and footnotes defined in another block may not resolve; a `.md` outside the workspaces or over 2 MB is preview-only. - Summary: DSH references at most three sessions per message, so the plugin sends batches; the AI writes the result with its file-writing tool. - PDFs with the same file name in different folders share one notes folder; section headings in the notes are always Chinese. ##

Development ```bash pixi run test # unit tests pixi run verify # contract and smoke tests ``` The plugin has two halves: the browser half `lib/client.js` and the host half `lib/index.js` and friends (registering the `/api/paper.*` routes), plus an optional Python sidecar `py/` used only to write highlights into the PDF file itself. Read [`AGENTS.md`](./AGENTS.md) (in Chinese) before developing: it covers the hard constraints on DSH plugins, the key APIs, the pitfalls hit so far and the roadmap. ##

Background and acknowledgement The author is a heavy user of [alphaXiv](https://www.alphaxiv.org/), which inspired this plugin's "ask about a selection, take notes in place" interaction. Its Q&A allowance is limited and its model can't be swapped, so this brings the "select → ask → note" loop into DSH, an environment you fully control: no new reader, just DSH's native preview, sessions and model configuration. _{PaperForge is not affiliated with, sponsored by or endorsed by alphaXiv or its team, and contains none of its code or assets.} ##