dsh-zotero 0.3.1 → 0.4.0

package/README.en.md

@@ -1,224 +1,130 @@
-<h1 align="center">dsh-zotero</h1>
+<div align="center">
 
+# dsh-zotero
+
+<img
+  src="https://readme-typing-svg.demolab.com?font=JetBrains+Mono&weight=500&size=18&pause=2000&color=CC2936&center=true&vCenter=true&width=760&lines=%3E+Zotero+as+an+evidence+store+for+agents."
+  alt="dsh-zotero"
+/>
 <p align="center">
-  <b>English</b> · <a href="README.md"><b>中文</b></a>
+  <a href="https://www.npmjs.com/package/dsh-zotero"><img src="https://img.shields.io/npm/v/dsh-zotero" alt="npm version" style="max-width:100%;"></a>
+  <a href="https://www.npmjs.com/package/dsh-zotero"><img src="https://img.shields.io/npm/dm/dsh-zotero" alt="npm downloads" style="max-width:100%;"></a>
+  <a href="https://www.npmjs.com/package/dsh-zotero"><img src="https://img.shields.io/npm/l/dsh-zotero" alt="license" style="max-width:100%;"></a>
+  <a href="https://awesome-dsh-plugin.com"><img src="https://awesome-dsh-plugin.com/badge.svg" alt="Awesome DSH Plugin"></a>
 </p>
+</div>
 
 <p align="center">
-  <a href="https://awesome-dsh-plugin.com"><img src="https://awesome-dsh-plugin.com/badge.svg" alt="Awesome DSH Plugin"></a>
-  <img src="https://img.shields.io/npm/v/dsh-zotero" alt="npm version">
-  <img src="https://img.shields.io/npm/dm/dsh-zotero" alt="npm downloads">
-  <img src="https://img.shields.io/npm/l/dsh-zotero" alt="license">
+  <a href="README.md"><b>中文</b></a> · <b>English</b>
 </p>
 
-Let agents search, read, and cite your local [Zotero](https://www.zotero.org) library: find papers, browse notes and annotations, pull evidence by question, open the source document, generate citations.
+dsh-zotero is a [Zotero](https://www.zotero.org) plugin designed for agent research workflows. Agents can search your library directly, view metadata and notes, extract evidence passages relevant to a question, open source PDFs, and generate citations and bibliographies.
 
-Describe what you need in a session and the Agent calls the tools below as needed. The only manual command is `/zotero status`.
+<p align="center">
+  <img src="docs/images/header-collage.png" width="70%" alt="dsh-zotero UI: sources panel, evidence extraction, export view">
+</p>
 
 ## Tools
 
-| Tool                | Purpose                                                                                                                               |
-| ------------------- | ------------------------------------------------------------------------------------------------------------------------------------- |
-| `zotero_search`     | Discover: search by title/creator/year, or indexed full text with `everything`; optionally scope to a collection or saved search.     |
-| `zotero_get`        | Inspect: read one item's structured core metadata, optionally with manifests and previews of its notes, annotations, and attachments. |
-| `zotero_retrieve`   | Evidence: return the most relevant bounded evidence passages (annotations, notes, abstract, full-text chunks) for a query.            |
-| `zotero_attachment` | Source: resolve an item or attachment ref to the original attachment's verified on-disk path or linked URL.                           |
-| `zotero_export`     | Cite: let Zotero's own citation/export machinery produce citations, a CSL bibliography, or `bibtex` / `biblatex` / `ris` / `csljson`. |
-
-## Usage example
+| Tool                | Purpose                                                                         |
+| ------------------- | ------------------------------------------------------------------------------- |
+| `zotero_search`     | Search by title/creator/year; `everything` mode also searches indexed full text |
+| `zotero_get`        | Read one item's metadata, optionally with notes, annotations, and attachments   |
+| `zotero_retrieve`   | Return the most relevant evidence passages for a query                          |
+| `zotero_attachment` | Resolve a ref to a verified on-disk path or linked URL                          |
+| `zotero_export`     | Generate citations, bibliographies, BibTeX/BibLaTeX/RIS/CSL JSON                |
 
-The Agent moves down the ladder as a request deepens. A typical conversation:
-
-> User: "Find papers about FlashAttention."
-> Agent → `zotero_search`, returning candidates with refs.
->
-> User: "What is the first one? Have I read it before?"
-> Agent → `zotero_get`: metadata, 17 annotations, 2 notes, limited previews.
->
-> User: "What did I think about its evaluation?"
-> Agent → `zotero_retrieve(query:"evaluation", sources:["annotations","notes"])`, returning matching note and annotation evidence.
->
-> User: "How does the paper itself explain memory efficiency?"
-> Agent → `zotero_retrieve(query:"memory efficiency", sources:["fulltext","abstract"])`, returning abstract and full-text passages.
->
-> User: "Show me the original PDF."
-> Agent → `zotero_attachment(item ref)`, returning the verified file path; if the composition has a PDF/file reader, the Agent hands it off for further analysis.
->
-> User: "Generate an APA bibliography for these three."
-> Agent → `zotero_export(format:"bibliography", style:"apa")`.
-
-## Command
-
-`/zotero status` reports connectivity, API/schema versions, and the database identity (Server ID, Zotero 10+). This is the only health check. Ordinary calls fail with typed domain errors.
-
-## Requirements
-
-- Zotero desktop with the local API enabled: **Settings → Advanced → "Allow other applications on this computer to communicate with Zotero"**.
-- Read access is unauthenticated on `http://127.0.0.1:23119/api`. V1 has no path that modifies library data (items, notes, tags, collections).
-- Zotero ≥ 7 speaking local API version 3. Upgrade if the status command reports a version mismatch.
+[Full tool reference →](docs/tools.md)
 
 ## Install
 
-### By package name
-
 ```sh
 dsh plugin --profile <name> add dsh-zotero
 ```
 
-The tarball ships the built `lib/` (the node half plus the browser half `lib/client.js`); no local build is needed. The browser half is the configuration card: dsh web scans the package's `dsh.client` manifest and mounts it automatically, with no extra setup.
-
-### From a local tarball
+From GitHub source:
 
 ```sh
-cd dsh-zotero
-npm pack
-dsh plugin --profile <name> add ./dsh-zotero-0.1.0.tgz
+dsh plugin --profile <name> add github:Vncntvx/dsh-zotero
 ```
 
-`npm pack` runs `prepare` first, so the tarball carries a fresh `lib/`. Use this for unpublished or local trial installs.
-
-### From the GitHub source
+From a local tarball:
 
 ```sh
-dsh plugin --profile <name> add github:Vncntvx/dsh-zotero
+cd dsh-zotero && npm pack
+dsh plugin --profile <name> add ./dsh-zotero-*.tgz
 ```
 
-A git install fetches sources instead of built artifacts, so pnpm installs the dependencies and then runs this package's `prepare` to build in place (TypeScript and `@types/node` live in `dependencies`). pnpm ≥ 10 refuses to run a git dependency's `prepare` by default, so the first `add` fails and points at the fix: add the package key to the profile's `pnpm-workspace.yaml` and re-run:
-
-```yaml
-allowBuilds:
-  dsh-zotero: true
-```
+After installing, start a new session so the agent picks up the Zotero tools.
 
-`allowBuilds` grants permission to run the package's code on your machine at install time. Only allow sources you trust, and prefer pinning a commit (`github:Vncntvx/dsh-zotero#<sha>`).
+The plugin provides a settings card under **Settings → Plugins** where you can adjust the API address, concurrency limits, full-text retrieval toggle, and more. Changes take effect on save. See [Configuration](docs/configuration.md).
 
-The plugin mounts as id `zotero` and takes effect on the next dsh start. After installing or enabling the plugin, start a new session if the current one was created before the plugin loaded, so the Agent picks up the Zotero tools.
+[Installation details →](docs/getting-started.md)
 
-## Configuration
+## Requirements
 
-All values are `Config` fields changeable from the bundle's `config` block (e.g. via `dsh plugin config`). Defaults are shown.
+- Zotero ≥ 7 with local API enabled: **Settings → Advanced → "Allow other applications on this computer to communicate with Zotero"**
+- Node.js ≥ 22.19 (or ≥ 24)
+- Local API at `http://127.0.0.1:23119/api`, unauthenticated, read-only
 
-| Field                  | Default                      | Meaning                                                                                                        |
-| ---------------------- | ---------------------------- | -------------------------------------------------------------------------------------------------------------- |
-| `baseUrl`              | `http://127.0.0.1:23119/api` | Local API base URL. Plain loopback HTTP only.                                                                  |
-| `provider`             | `local`                      | Provider id to select.                                                                                         |
-| `timeoutMs`            | `5000`                       | Per-request provider deadline.                                                                                 |
-| `maxSearchResults`     | `20`                         | Upper bound for `zotero_search` `limit`.                                                                       |
-| `maxNoteScanRecords`   | `200`                        | Upper bound for note records scanned for body matches by `zotero_search`.                                      |
-| `maxEvidenceChars`     | `6000`                       | Total character budget for retrieved evidence.                                                                 |
-| `maxEvidencePassages`  | `4`                          | Upper bound for evidence passage counts.                                                                       |
-| `maxDetailChars`       | `3000`                       | Character budget for `zotero_get` abstract previews.                                                           |
-| `maxNoteBodyChars`     | `30000`                      | Character budget for a note item's own body returned by `zotero_get`.                                          |
-| `maxNoteChars`         | `2000`                       | Character budget per note preview in `zotero_get`.                                                             |
-| `maxNoteRecords`       | `50`                         | Upper bound for note records returned by `zotero_get`.                                                         |
-| `maxAnnotationRecords` | `100`                        | Upper bound for annotation records returned by `zotero_get`.                                                   |
-| `fulltextChunkWords`   | `200`                        | Word count per full-text passage entering evidence ranking.                                                    |
-| `maxFulltextChars`     | `250000`                     | Full text accepted into evidence ranking.                                                                      |
-| `maxResponseBytes`     | `16777216`                   | Streaming byte bound for every API response.                                                                   |
-| `maxExportChars`       | `1000000`                    | Export output hard limit. Never mid-truncated.                                                                 |
-| `maxExportRefs`        | `1000`                       | Upper bound for refs in one `zotero_export` call; keeps the request line under the server's HTTP header limit. |
-| `defaultStyle`         | `apa`                        | CSL style for citation/bibliography formats.                                                                   |
-| `defaultLocale`        | `en-US`                      | CSL locale for citation/bibliography formats.                                                                  |
-| `webEnabled`           | `true`                       | Enables the dedicated Zotero conversation tab; the gate is read once per page load.                            |
+## Usage example
 
-### Web configuration
+The agent calls tools step by step during a conversation. Each result becomes context for the next step.
 
-The plugin registers a "Zotero" card in dsh web's **Settings → Plugins → Plugin configuration** page listing all 20 fields above. The card binds the `zotero` settings namespace: writes land in the `zotero:` section of `$DSH_HOME/settings.yaml` (layered over the patch entry's `config`, user layer wins), and **saves apply live** — the transport and the provider rebuild on the new values, so the next tool call or `/zotero status` uses them without a dsh restart.
+```text
+User: Find papers about Risk
+Agent → zotero_search(query: "Risk", itemType: "journalArticle")
+       5 matches; user picks the first 3
 
-- Invalid values (a non-loopback `baseUrl`, a non-positive limit) are refused before the write; the card reports the failed save and keeps the draft, and the plugin keeps running on the last valid value.
-- Every field shows its effective value; fields overridden by the settings document carry an "Overridden" badge and offer a one-click reset (clears the user layer, back to the patch entry value).
-- External edits to the settings document (e.g. editing `settings.yaml` directly) hot-apply too.
-- Compositions without a settings service (pure headless) never register the namespace, and the plugin behaves exactly as if unconfigured.
+User: What does the first one's abstract say?
+Agent → zotero_get(ref: 1, fields: ["abstractNote"])
+       Returns the full abstract
 
-### Web view
+User: Find the methodology discussion in this paper
+Agent → zotero_retrieve(query: "methodology", sources: ["fulltext", "notes"])
+       Returns relevant passages with page numbers
 
-The dsh web session view is a tab ring (Chat, Trajectory, …). The plugin registers a dedicated **Zotero** tab (`conversation.view`, id `zotero`, after Trajectory and dsh-context) and leaves dsh's built-in chat and trajectory display untouched:
+User: Export all three as BibTeX
+Agent → zotero_export(refs: [1,2,3], format: "bibtex")
+       Generates BibTeX entries, ready to copy or download
+```
 
-- A **connection strip** leads the tab: one status probe on mount, another per explicit Refresh (request-driven, no polling timers); it shows the connection state, API/schema versions, Server ID (Zotero 10+), and the last-checked time, with the diagnosis when Zotero is unavailable.
-- Below it, the session's **Zotero tool activity**: every search, read, retrieve, attachment, and export call renders as a rich card (expandable, copyable refs, evidence passages labeled by source), fully replay-driven from the conversation snapshot — the same transcript renders the same cards, and missing meta degrades to the raw content.
-- The **Web → Session tool cards** toggle in the settings page (`webEnabled`, default on) controls the tab's registration; the gate is read once per page load, so a toggle change applies after the page reloads. When off, Zotero calls show as dsh's built-in generic cards in the trajectory.
+More examples in [Features](docs/features.md).
 
 ## Limits
 
-- Read-only library: no path modifies items, notes, tags, or collections.
-- Full-text evidence depends on Zotero's index: `everything` search and `retrieve` full-text passages both require indexing.
-- Note-content search is a client-side scan: library/collection scopes and the first result page only, bounded by `maxNoteScanRecords`; notes beyond the cap never match.
-- Attachment depth depends on the harness composition: `zotero_attachment` returns the file location; reading that PDF further needs a matching file/PDF capability.
-- Evidence ranking is term-based relevance, not embedding or semantic search.
+- **Read-only library**: all operations are reads; items, notes, tags, and collections are unchanged
+- **Loopback only**: network requests go only to `127.0.0.1:23119`
+- **Evidence ranking is term-based**: BM25 ranks passages by query-term frequency match
+- **Exports are static text**: returned as text, ready to copy into your target document
+- **Full-text evidence depends on Zotero's index**: unindexed PDFs yield no full-text passages
+- **Attachment depth depends on the harness**: `zotero_attachment` returns the file location; reading the PDF further needs a matching host capability
+
+## Documentation
+
+| Doc                                        | Covers                                                 |
+| ------------------------------------------ | ------------------------------------------------------ |
+| [Getting Started](docs/getting-started.md) | Installation, prerequisites, first verification        |
+| [Features](docs/features.md)               | Sources panel, chat integration, evidence, exports     |
+| [Tool Reference](docs/tools.md)            | Parameters, return values, error codes for all 5 tools |
+| [Configuration](docs/configuration.md)     | 20 config fields, defaults, hot-reload                 |
+| [Architecture](docs/architecture.md)       | Data flow, layer responsibilities, design boundaries   |
+| [Development](docs/development.md)         | Build, test, local development                         |
+| [Troubleshooting](docs/troubleshooting.md) | 11 common issues with symptoms and fixes               |
 
 ## Development
 
-### Commands
-
 ```sh
-npm install                      # uses a local npm cache (see the workspace note below)
-npm test                         # unit tests (mock Zotero server + browser card tests)
-npm run test:coverage            # 100% coverage gate on src/
-npm run typecheck                # tsc --noEmit, node / test / client projects
-npm run build                    # tsc emits the node half into lib/; esbuild emits the browser half lib/client.js
-npm run build:client             # rebuild the browser half only (self-checks the loader handoff)
-npm run dev:client               # watch the browser half (pair with the hot-swap overlay)
-npm run format                   # prettier --write across the repo
-npm run format:check             # verify formatting (run before committing)
+npm install --no-workspaces   # this repo lives inside the deepseek-harness workspace
+npm test                      # vitest unit tests against the mock Zotero server
+npm run typecheck             # tsc --noEmit for node, test, and client projects
+npm run build                 # tsc emits node half into lib/; esbuild emits browser half lib/client.js
+npm run dev                   # tsc --watch for host half hot reload
+npm run dev:client            # esbuild --watch for browser half hot reload
 ```
 
-> This checkout sits inside the deepseek-harness workspace tree: the parent `package.json` declares `workspaces`, so npm walks up to it and tries to install the whole workspace. Run `npm install --no-workspaces` instead (or drop a `.npmrc` with `workspaces=false` in this repository).
-
-Integration tests run against a live Zotero and stay skipped unless enabled:
-
-```sh
-npm run test:integration
-# or: ZOTERO_INTEGRATION=1 npx vitest run tests/integration/zotero.integration.spec.ts
-```
-
-### Running locally
-
-#### From a dsh source checkout
-
-Build the checkout once (`pnpm install && pnpm run build`), then load the plugin source through the dev overlay:
-
-```sh
-pnpm dsh web --patch ./dsh-zotero/dev.cordis.yml
-```
-
-`dev.cordis.yml` points the plugin entry at the absolute `src/index.ts`. The dsh source launch loads that TypeScript entry through tsx, so the plugin requires no prebuild. Update the absolute path when the checkout location differs.
-
-#### With the npm-installed dsh
-
-This plugin builds in two halves: the **Node side** (`lib/`, emitted by `tsc`, holds the service, tools, provider, and other logic) and the **browser side** (`lib/client.js`, emitted by `esbuild`, holds the dsh web configuration card and the Zotero tab view). The three flows below cover the common cases.
-
-- `npm run build` emits both halves; `npm run build:client` rebuilds only the browser side.
-- The rest of this section assumes `npm run build` has been run at least once so `lib/` exists.
-
-**① Resident instance verification (tarball install)**
-
-Pack a tarball and install it into a profile. The plugin runs from the tarball's built artifacts; code updates require re-packing and re-installing. Verify with the production-stack smoke after install:
-
-```sh
-npm pack
-dsh plugin --profile <name> add ./dsh-zotero-0.1.0.tgz
-cd ~/.dsh/profiles/<name>
-node --input-type=module < /path/to/dsh-zotero/scripts/smoke.mjs
-```
-
-The smoke must be run inside the profile directory, so bare imports resolve from the profile's flat `node_modules`. It verifies `status`, `search`, `get`, `retrieve`, `export`, the policy prompt section, and the registration of all five tools; `SMOKE PASS` indicates the packed plugin passes the installed-path checks.
-
-**② Node-side hot-swap development**
-
-The `dev-lib.cordis.yml` overlay disables the profile's tarball row (id `zotero`), inserts a `zotero-dev` row pointing at this checkout's `lib/index.js`, and re-enables HMR. The production web profile disables loader HMR by default, and HMR's watch root lives in the profile directory, so the overlay sets `base` explicitly. When the build output changes, HMR disposes the old instance and reconstructs the plugin in the same process — no dsh restart needed:
-
-```sh
-cd ./dsh-zotero                 # from the deepseek-harness checkout
-npm run dev &                    # tsc --watch: rebuild lib on src changes
-dsh web --patch ./dev-lib.cordis.yml --port 3307
-```
-
-Hot swap only affects the instance started with `--patch`; the resident instance keeps running the tarball version, independently.
-
-**③ Browser-side development**
-
-The web frontend only scans loader rows whose `name` is a bare package name (npm-resolvable to `package.json`) to load the browser-side bundle. `dev-lib.cordis.yml` uses an absolute-path row, which does not trigger browser-side loading, so the card does not appear in the ② dev instance. To develop the card, first install this checkout into the profile (`npm install <this repo path>` as a `file:` dependency, or pack and install the tarball), then pair `npm run dev:client` (esbuild watch) with the hot-swap overlay: browser-bundle changes make HMR re-fetch `/plugins/dsh-zotero/client.js`.
+Build output splits into `lib/` (Node side) and `lib/client.js` (browser side — settings card + Zotero tab). For full plugin development with both halves, use the `dev-lib.cordis.yml` overlay. See [Development](docs/development.md) for details.
 
 ## License
 
-MIT. See [LICENSE](./LICENSE).
+[MIT](./LICENSE) — free to use, modify, and distribute.

package/README.md

@@ -1,221 +1,130 @@
-<h1 align="center">dsh-zotero</h1>
+<div align="center">
 
+# dsh-zotero
+
+<img
+  src="https://readme-typing-svg.demolab.com?font=JetBrains+Mono&weight=500&size=22&pause=2000&color=CC2936&center=true&vCenter=true&width=760&lines=%3E+Zotero+as+an+evidence+store+for+agents."
+  alt="dsh-zotero"
+/>
 <p align="center">
-  <a href="README.en.md"><b>English</b></a> · <b>中文</b>
+  <a href="https://www.npmjs.com/package/dsh-zotero"><img src="https://img.shields.io/npm/v/dsh-zotero" alt="npm version" style="max-width:100%;"></a>
+  <a href="https://www.npmjs.com/package/dsh-zotero"><img src="https://img.shields.io/npm/dm/dsh-zotero" alt="npm downloads" style="max-width:100%;"></a>
+  <a href="https://www.npmjs.com/package/dsh-zotero"><img src="https://img.shields.io/npm/l/dsh-zotero" alt="license" style="max-width:100%;"></a>
+  <a href="https://awesome-dsh-plugin.com"><img src="https://awesome-dsh-plugin.com/badge.svg" alt="Awesome DSH Plugin"></a>
 </p>
+</div>
 
 <p align="center">
-  <a href="https://awesome-dsh-plugin.com"><img src="https://awesome-dsh-plugin.com/badge.svg" alt="Awesome DSH Plugin"></a>
-  <img src="https://img.shields.io/npm/v/dsh-zotero" alt="npm version">
-  <img src="https://img.shields.io/npm/dm/dsh-zotero" alt="npm downloads">
-  <img src="https://img.shields.io/npm/l/dsh-zotero" alt="license">
+  <a href="README.en.md"><b>English</b></a> · <b>中文</b>
 </p>
 
-让 Agents 搜索、阅读并引用你的本地 [Zotero](https://www.zotero.org) 文献库：找文献、查看笔记与批注、按问题取证、打开原文、生成引用。
+dsh-zotero 是面向 Agent 研究工作流的 [Zotero](https://www.zotero.org) 插件。Agent 可以直接从你的文献库中搜索文献、查看元数据和笔记、提取与问题相关的证据段落、打开原文 PDF，并生成引用和参考文献表。
 
-在会话里用自然语言描述需求，Agent 自动按需调用下面的工具；唯一的手动命令是 `/zotero status`。
+<p align="center">
+  <img src="docs/images/header-collage.png" width="70%" alt="dsh-zotero 界面：来源面板、证据提取、导出视图">
+</p>
 
 ## 工具
 
-| 工具                | 用途                                                                                                                       |
-| ------------------- | -------------------------------------------------------------------------------------------------------------------------- |
-| `zotero_search`     | 发现：按标题/作者/年份搜索库里的资料，`everything` 模式连全文索引一起搜；可限定某个分类或已保存搜索                        |
-| `zotero_get`        | 检查：读取一条资料的结构化核心元数据，可选检查笔记、注释、附件的清单与预览。                                               |
-| `zotero_retrieve`   | 取证：按问题返回最相关的有界证据片段（注释、笔记、摘要、全文分块）                                                         |
-| `zotero_attachment` | 原文：解析条目或附件 ref，返回原始附件已验证的磁盘路径或链接 URL                                                           |
-| `zotero_export`     | 引用：让 Zotero 按自己的 citation/export 能力生成结果（引用、CSL 参考文献表、`bibtex` / `biblatex` / `ris` / `csljson`）。 |
-
-## 使用示例
-
-Agent 按需求逐层深入，一段典型对话：
-
-> 用户：「帮我找 FlashAttention 相关论文」
-> Agent → `zotero_search`，返回候选条目与 ref。
->
-> 用户：「第一篇是什么？我以前读过吗？」
-> Agent → `zotero_get`：元数据、17 条批注、2 条笔记与有限预览。
->
-> 用户：「我当时对 evaluation 有什么意见？」
-> Agent → `zotero_retrieve(query:"evaluation", sources:["annotations","notes"])`，返回相关笔记与批注证据。
->
-> 用户：「论文自己怎么解释 memory efficiency？」
-> Agent → `zotero_retrieve(query:"memory efficiency", sources:["fulltext","abstract"])`，返回摘要与全文片段。
->
-> 用户：「我要看原 PDF」
-> Agent → `zotero_attachment(条目 ref)`，返回已验证的文件路径；若当前 Harness 配置了 PDF/file 读取能力，再交给该能力继续分析。
->
-> 用户：「把这三篇生成 APA 参考文献表」
-> Agent → `zotero_export(format:"bibliography", style:"apa")`。
-
-## 命令
-
-`/zotero status` 报告连通性、API/schema 版本和数据库身份标识（Server ID，Zotero 10+）。这是唯一的健康检查。普通调用失败时返回带类型的领域错误。
+| 工具                | 用途                                                    |
+| ------------------- | ------------------------------------------------------- |
+| `zotero_search`     | 按标题/作者/年份搜索，`everything` 模式连全文索引一起搜 |
+| `zotero_get`        | 读取单条文献的元数据，可选返回笔记、批注、附件清单      |
+| `zotero_retrieve`   | 按查询词返回最相关的证据段落（批注/笔记/摘要/全文）     |
+| `zotero_attachment` | 将文献 ref 解析为已验证的磁盘路径或链接 URL             |
+| `zotero_export`     | 生成引用、参考文献表、BibTeX/BibLaTeX/RIS/CSL JSON      |
 
-## 环境要求
-
-- 已安装 Zotero 桌面版，并启用本地 API：**设置 → 高级 → “Allow other applications on this computer to communicate with Zotero”**。
-- 本地 API 为无认证读取，地址为 `http://127.0.0.1:23119/api`。V1 没有任何修改文献库数据（条目、笔记、标签、分类等）的路径。
-- Zotero ≥ 7，本地 API 版本为 3。如果 status 命令报告版本不匹配，请升级。
+[完整工具参考 →](docs/tools.md)
 
 ## 安装
 
-### 按包名安装
-
 ```sh
 dsh plugin --profile <name> add dsh-zotero
 ```
 
-tarball 内含已构建的 `lib/`（node 半与浏览器半 `lib/client.js`），无需本地构建。浏览器半边是配置卡片：dsh web 会扫描到包内声明的 `dsh.client` 清单并自动挂载，无需额外配置。
-
-### 本地 tarball
-
-```sh
-cd dsh-zotero
-npm pack
-dsh plugin --profile <name> add ./dsh-zotero-0.1.0.tgz
-```
-
-`npm pack` 先运行 `prepare` 构建 `lib/`，适合未发布或本地试装。
-
-### 从 GitHub 源码安装
+从 GitHub 源码安装：
 
 ```sh
 dsh plugin --profile <name> add github:Vncntvx/dsh-zotero
 ```
 
-git 安装拉取源码而非构建产物，pnpm 安装依赖后运行本包的 `prepare` 现场构建（TypeScript 与 `@types/node` 在 `dependencies` 中）。pnpm ≥ 10 默认拒绝运行 git 依赖的 `prepare`，首次 `add` 会失败并提示：把包名加进 profile 的 `pnpm-workspace.yaml` 后重新执行：
+本地 tarball：
 
-```yaml
-allowBuilds:
-  dsh-zotero: true
+```sh
+cd dsh-zotero && npm pack
+dsh plugin --profile <name> add ./dsh-zotero-*.tgz
 ```
 
-`allowBuilds` 授权该包在安装时执行代码，只允许你信任的来源，建议固定到具体提交（`github:Vncntvx/dsh-zotero#<sha>`）。
-
-插件以 id `zotero` 挂载，下次启动 dsh 时生效。安装或启用插件后，如果当前会话创建于插件加载之前，请新建会话，确保 Agent 获得 Zotero 工具。
-
-## 配置
-
-所有值都是 `Config` 字段，可在 bundle 的 `config` 块中修改（例如通过 `dsh plugin config`）。以下为默认值。
+安装后重启新建会话，Agent 即可使用 Zotero 工具。
 
-| 字段                   | 默认值                       | 含义                                                                                   |
-| ---------------------- | ---------------------------- | -------------------------------------------------------------------------------------- |
-| `baseUrl`              | `http://127.0.0.1:23119/api` | 本地 API 基础 URL。仅支持纯回环 HTTP。                                                 |
-| `provider`             | `local`                      | 要选择的 provider id。                                                                 |
-| `timeoutMs`            | `5000`                       | 每个请求的 provider 超时时间。                                                         |
-| `maxSearchResults`     | `20`                         | `zotero_search` `limit` 的上限。                                                       |
-| `maxNoteScanRecords`   | `200`                        | `zotero_search` 补扫笔记正文的笔记数量上限。                                           |
-| `maxEvidenceChars`     | `6000`                       | 检索证据的总字符预算。                                                                 |
-| `maxEvidencePassages`  | `4`                          | 证据片段数量的上限。                                                                   |
-| `maxDetailChars`       | `3000`                       | `zotero_get` 摘要预览的字符预算。                                                      |
-| `maxNoteBodyChars`     | `30000`                      | `zotero_get` 返回 note 条目自身正文的字符预算。                                        |
-| `maxNoteChars`         | `2000`                       | `zotero_get` 单条笔记预览的字符预算。                                                  |
-| `maxNoteRecords`       | `50`                         | `zotero_get` 返回笔记数量的上限。                                                      |
-| `maxAnnotationRecords` | `100`                        | `zotero_get` 返回批注数量的上限。                                                      |
-| `fulltextChunkWords`   | `200`                        | 进入证据排序的全文片段词数。                                                           |
-| `maxFulltextChars`     | `250000`                     | 进入证据排序的全文大小上限。                                                           |
-| `maxResponseBytes`     | `16777216`                   | 每个 API 响应的流式字节上限。                                                          |
-| `maxExportChars`       | `1000000`                    | 导出输出的硬上限。不会中途截断。                                                       |
-| `maxExportRefs`        | `1000`                       | 单次 `zotero_export` 的 refs 数量上限，保护请求行不超服务器 HTTP 头限制。              |
-| `defaultStyle`         | `apa`                        | 引用/参考文献使用的 CSL 样式。                                                         |
-| `defaultLocale`        | `en-US`                      | 引用/参考文献使用的 CSL locale。                                                       |
-| `webEnabled`           | `true`                       | 是否在会话顶部显示 Zotero 专属标签页；开关在每次页面加载时读取，切换后需刷新页面生效。 |
+插件在 **Settings → Plugins** 中提供配置卡片，可调整 API 地址、并发限制、全文检索开关等参数，保存即生效。详见 [配置](docs/configuration.md)。
 
-### Web 配置
+[安装详情 →](docs/getting-started.md)
 
-插件在 dsh web 的 **Settings → Plugins → Plugin configuration** 页面注册一张 "Zotero" 卡片，列出上表全部字段。卡片绑定 `zotero` 设置命名空间：写入落在 `$DSH_HOME/settings.yaml` 的 `zotero:` 小节（叠加在 patch 条目 `config` 之上，用户层优先），**保存即时生效**——传输层与 provider 按新值重建，下一次工具调用或 `/zotero status` 无需重启 dsh 即可使用。
+## 前置条件
 
-- 非法值（非回环 `baseUrl`、非正数上限）在写入前被拒绝；卡片提示保存失败并保留草稿，插件继续运行在最后一个合法值上。
-- 每个字段显示有效值；被设置文档覆盖的字段带有 "Overridden" 徽标，提供一键重置（清除用户层，回到 patch 条目值）。
-- 直接编辑设置文档（如手工修改 `settings.yaml`）同样热生效。
-- 没有设置服务的组合（纯 headless）不会注册命名空间，插件行为与未配置时完全一致。
+- Zotero ≥ 7 桌面版，启用本地 API：**设置 → 高级 → "允许其他应用程序与 Zotero 通信"**
+- Node.js ≥ 22.19（或 ≥ 24）
+- 本地 API 地址 `http://127.0.0.1:23119/api`，无认证，只读
 
-### Web 视图
-
-dsh web 的会话视图是标签页环（Chat、Trajectory、…）。插件注册一个专属 **Zotero** 标签页（`conversation.view`，id `zotero`，位于 Trajectory 与 dsh-context 之后），不触碰 dsh 自带的聊天与轨迹视图：
-
-- 标签页顶部是**连接条**：挂载时探测一次、每次手动刷新再探测一次（请求驱动，无轮询定时器）；显示连接状态、API/Schema 版本、Server ID（Zotero 10+）与上次检查时间；Zotero 不可用时显示诊断信息。
-- 下方是本会话的 **Zotero 工具活动**：每次搜索、精读、取证、附件解析与导出调用都渲染为富卡片（可展开、ref 可复制、证据段落标注来源），完全由会话快照重放驱动——同一段记录永远渲染出同样的卡片，meta 缺失时降级为原始内容。
-- 设置页的 **Web → 会话工具卡片** 开关（`webEnabled`，默认开启）控制标签页的注册；开关在每次页面加载时读取一次，切换后需刷新页面生效。关闭后，Zotero 调用在轨迹中显示为 dsh 内置的通用卡片。
-
-### 限制
-
-- 只读文献库：没有任何路径会修改条目、笔记、标签或合集。
-- 全文证据依赖 Zotero 的索引：`everything` 搜索与 `retrieve` 的全文段落都需要已建立索引。
-- 笔记正文搜索是客户端扫描：仅限 library/collection 作用域与第一页结果，受 `maxNoteScanRecords` 限制；超出上限的笔记永远不会命中。
-- 附件深度取决于宿主组合：`zotero_attachment` 返回文件位置；继续阅读该 PDF 需要宿主具备对应的文件/PDF 能力。
-- 证据排序是基于词项的相关性，而非向量或语义检索。
-
-## 开发
-
-### 命令
-
-```sh
-npm install                      # 使用本地 npm 缓存（见下方 workspace 说明）
-npm test                         # 单元测试（mock Zotero server + 浏览器卡片测试）
-npm run test:coverage            # 对 src/ 的 100% 覆盖率门禁
-npm run typecheck                # tsc --noEmit，node / test / client 三个项目
-npm run build                    # tsc 生成 node 半 lib/ + esbuild 生成浏览器半 lib/client.js
-npm run build:client             # 只重建浏览器半（含 loader 交接格式自检）
-npm run dev:client               # 浏览器半 watch 模式（配合热替换 overlay）
-npm run format                   # prettier --write 全仓格式化
-npm run format:check             # 校验格式化（提交前执行）
-```
-
-> 本仓库位于 deepseek-harness workspace 树内：父目录 `package.json` 声明了 `workspaces`，npm 会向上找到它并尝试安装整个 workspace。请使用 `npm install --no-workspaces`（或在本仓库放置含 `workspaces=false` 的 `.npmrc`）。
-
-集成测试面向真实 Zotero，默认跳过，需显式开启：
+## 使用示例
 
-```sh
-npm run test:integration
-# 或：ZOTERO_INTEGRATION=1 npx vitest run tests/integration/zotero.integration.spec.ts
-```
+Agent 在对话中根据用户需求逐步调用工具，每次调用的结果作为下一步的上下文。
 
-### 本地启动
+```text
+用户：帮我找 Risk 相关的论文
+Agent → zotero_search(query: "Risk", itemType: "journalArticle")
+       5 篇匹配结果，用户选择前 3 篇
 
-#### 从 dsh 源码启动
+用户：第一篇的摘要说了什么？
+Agent → zotero_get(ref: 1, fields: ["abstractNote"])
+       返回摘要全文
 
-在 deepseek-harness 源码 checkout 中构建一次（`pnpm install && pnpm run build`），然后通过 dev overlay 加载插件源码：
+用户：这篇里关于方法论的讨论，帮我找出来
+Agent → zotero_retrieve(query: "methodology", sources: ["fulltext", "notes"])
+       返回相关段落，带页码和来源
 
-```sh
-pnpm dsh web --patch ./dsh-zotero/dev.cordis.yml
+用户：把这三篇导出为 BibTeX
+Agent → zotero_export(refs: [1,2,3], format: "bibtex")
+       生成 BibTeX 条目，可复制或下载
 ```
 
-`dev.cordis.yml` 将插件入口指向绝对的 `src/index.ts`。dsh 的源码启动经 tsx 加载该 TypeScript 入口，插件因此无需预构建；若 checkout 路径不同，需同步修改文件中的绝对路径。
-
-#### 使用 npm 安装的 dsh
-
-本插件分两部分构建：**Node 端**（`lib/`，由 `tsc` 生成，包含服务、工具、provider 等逻辑）与**浏览器端**（`lib/client.js`，由 `esbuild` 生成，包含 dsh web 的配置卡片与 Zotero 标签视图）。下面三种开发流程覆盖了不同场景。
+更多示例见 [功能概览](docs/features.md)。
 
-**① 常驻实例验证（tarball 安装）**
+## 限制
 
-打包为 tarball 并安装到 profile，插件以 tarball 内的构建产物运行；代码更新后需重新打包安装。安装后通过生产栈 smoke 脚本验证：
+- **只读文献库**：所有操作均为读取，不修改条目、笔记、标签或分类
+- **只访问本机**：网络请求仅发往 `127.0.0.1:23119`
+- **证据排序是词项相关性**：基于 BM25，按查询词与 passage 的词频匹配度排序
+- **导出是静态文本**：以文本形式返回，需要手动复制到目标位置
+- **全文证据依赖 Zotero 索引**：未索引的 PDF 无法提供全文段落
+- **附件深度取决于宿主**：`zotero_attachment` 返回文件位置，继续阅读 PDF 需要宿主具备对应能力
 
-```sh
-npm pack
-dsh plugin --profile <name> add ./dsh-zotero-0.1.0.tgz
-cd ~/.dsh/profiles/<name>
-node --input-type=module < /path/to/dsh-zotero/scripts/smoke.mjs
-```
-
-smoke 脚本必须在 profile 目录内运行，这样裸导入才能从 profile 的扁平 `node_modules` 中解析。脚本依次验证 `status`、`search`、`get`、`retrieve`、`export`、策略提示词分区，以及五个工具的注册情况；输出 `SMOKE PASS` 表示打包后的插件通过了安装路径验证。
+## 文档
 
-**② Node 端热替换开发**
+| 文档                                | 内容                               |
+| ----------------------------------- | ---------------------------------- |
+| [快速上手](docs/getting-started.md) | 安装、前置条件、首次验证           |
+| [功能概览](docs/features.md)        | 来源面板、对话集成、证据提取、导出 |
+| [工具参考](docs/tools.md)           | 5 个工具的参数、返回值、错误码     |
+| [配置](docs/configuration.md)       | 20 个配置字段、默认值、热更新      |
+| [架构](docs/architecture.md)        | 数据流、各层职责、设计边界         |
+| [开发指南](docs/development.md)     | 构建、测试、本地开发               |
+| [问题排查](docs/troubleshooting.md) | 11 个常见问题的症状和处理          |
 
-`dev-lib.cordis.yml` 覆盖层会禁用 profile 中的 tarball 行（id `zotero`），转而插入 `zotero-dev` 行指向本仓库的 `lib/index.js`，并重新启用 HMR。生产 web profile 默认关闭 loader HMR，且 HMR 的监视根位于 profile 目录，因此覆盖层显式设置了 `base`。构建产物变化后，HMR 会在同一进程内销毁旧实例并重新构造插件，无需重启 dsh：
+## 开发
 
 ```sh
-cd ./dsh-zotero                 # 从 deepseek-harness checkout 进入本仓库
-npm run dev &                    # tsc --watch：修改 src 后自动重建 lib
-dsh web --patch ./dev-lib.cordis.yml --port 3307
+npm install --no-workspaces   # 本仓库在 deepseek-harness 工作区内，需要加 --no-workspaces
+npm test                      # 单元测试（vitest，mock Zotero 服务器）
+npm run typecheck             # tsc --noEmit，覆盖 node、test、client 三个项目
+npm run build                 # tsc 编译 node 部分到 lib/，esbuild 编译浏览器部分到 lib/client.js
+npm run dev                   # tsc --watch，host half 热更新
+npm run dev:client            # esbuild --watch，浏览器部分热更新
 ```
 
-热替换仅对通过 `--patch` 启动的实例生效；常驻实例仍运行 tarball 版本，互不影响。
-
-**③ 浏览器端开发**
-
-dsh web 只会扫描 Loader 行中 `name` 为裸包名（npm 能解析到 `package.json`）的条目来加载浏览器端 bundle。`dev-lib.cordis.yml` 使用的是绝对路径行，不会触发浏览器端加载，因此卡片不会出现在 ② 的 dev 实例中。开发卡片时需要先把本仓库装进 profile（`npm install <本仓库路径>` 作为 `file:` 依赖，或 `npm pack` 后安装 tarball），再配合 `npm run dev:client`（esbuild watch）与热替换 overlay 一起使用：浏览器 bundle 变化会触发 HMR 重新拉取 `/plugins/dsh-zotero/client.js`。
+构建产物分两部分：`lib/` 是 Node 侧代码，`lib/client.js` 是浏览器侧（settings 卡片 + Zotero tab）。本地开发推荐用 `dev-lib.cordis.yml` overlay 实现完整插件流程，详见 [开发指南](docs/development.md)。
 
 ## 许可证
 
-本插件以 [MIT](./LICENSE) 许可证发布。
+[MIT](./LICENSE) — 自由使用、修改和分发。