Fix configurable Lite setup paths

AGENTS.md

@@ -13,7 +13,7 @@
 [ ] Python 依赖已安装 (pip install requests pymupdf pillow)
 [ ] PaddleOCR API Key 已配置（在 .env 中）
 [ ] 目录结构已创建（setup.py 会自动完成）
-[ ] Zotero 数据目录已链接到 99_System/Zotero
+[ ] Zotero 数据目录已链接到 <system_dir>/Zotero
 ```
 
 ### Better BibTeX 自动导出配置
@@ -21,7 +21,7 @@
 1. Zotero → Edit → Preferences → Better BibTeX
 2. 勾选 **"Keep updated"**（自动导出）
 3. 选择导出格式：**Better BibLaTeX** 或 **Better BibTeX**
-4. 导出路径设置为：`{你的Vault路径}/99_System/PaperForge/exports/library.json`
+4. 导出路径设置为：`{你的Vault路径}/<system_dir>/PaperForge/exports/library.json`
 5. 点击 OK，JSON 文件会自动生成并保持同步
 
 ---
@@ -47,13 +47,13 @@ PaperForge Lite 采用 **两层设计**：
 ```
 Zotero 添加文献
     ↓ Better BibTeX 自动导出 JSON
-99_System/PaperForge/exports/library.json
+<system_dir>/PaperForge/exports/library.json
     ↓ 运行 selection-sync
-03_Resources/LiteratureControl/library-records/<domain>/<key>.md
+<resources_dir>/<control_dir>/library-records/<domain>/<key>.md
     ↓ 运行 index-refresh
-03_Resources/Literature/<domain>/<key> - <Title>.md（正式笔记）
+<resources_dir>/<literature_dir>/<domain>/<key> - <Title>.md（正式笔记）
     ↓ 用户在 library-record 中设置 do_ocr: true
-运行 ocr → 99_System/PaperForge/ocr/<key>/
+运行 ocr → <system_dir>/PaperForge/ocr/<key>/
     ↓ 用户在 library-record 中设置 analyze: true
 运行 deep-reading（查看队列，确认就绪）
     ↓ 用户执行 Agent 命令
@@ -68,20 +68,20 @@ Zotero 添加文献
 
 ```
 {你的Vault根目录}/
-├── 03_Resources/
-│   ├── Literature/                    ← 正式文献笔记（index-refresh 生成）
+├── <resources_dir>/
+│   ├── <literature_dir>/                    ← 正式文献笔记（index-refresh 生成）
 │   │   ├── 骨科/
 │   │   ├── 运动医学/
 │   │   └── ...（你的分类）
-│   └── LiteratureControl/             ← 状态跟踪
+│   └── <control_dir>/             ← 状态跟踪
 │       └── library-records/           ← selection-sync 输出
 │           ├── 骨科/
 │           │   └── ABCDEFG.md         ← 单条文献状态记录
 │           └── 运动医学/
 │               └── HIJKLMN.md
 │
-├── 99_System/
-│   ├── LiteraturePipeline/
+├── <system_dir>/
+│   ├── PaperForge/
 │   │   ├── exports/                   ← Better BibTeX 自动导出的 JSON
 │   │   │   └── library.json
 │   │   ├── ocr/                       ← OCR 结果（每个文献一个子目录）
@@ -94,7 +94,7 @@ Zotero 添加文献
 │   │       └── literature_pipeline.py ← 核心脚本
 │   └── Zotero/                        ← Junction/Symlink 到 Zotero 数据目录
 │
-├── .opencode/                         ← OpenCode Agent 配置（自动创建）
+├── <agent_config_dir>/                         ← OpenCode Agent 配置（自动创建）
 │   └── skills/
 │       └── literature-qa/             ← 深度阅读 Skill
 │           ├── scripts/
@@ -110,11 +110,11 @@ Zotero 添加文献
 
 | 目录 | 内容 | 谁生成/修改 |
 |------|------|------------|
-| `03_Resources/Literature/` | 正式文献笔记（含 frontmatter + 精读内容） | index-refresh 生成，Agent 写入精读 |
-| `03_Resources/LiteratureControl/library-records/` | 文献状态跟踪（analyze, ocr_status 等） | selection-sync 生成，用户修改状态 |
-| `99_System/PaperForge/exports/` | Better BibTeX JSON 导出 | Zotero 自动导出 |
-| `99_System/PaperForge/ocr/` | OCR 全文 + 图表切割 | ocr worker 生成 |
-| `99_System/Zotero/` | Zotero 数据目录的链接 | 安装时手动创建 junction |
+| `<resources_dir>/<literature_dir>/` | 正式文献笔记（含 frontmatter + 精读内容） | index-refresh 生成，Agent 写入精读 |
+| `<resources_dir>/<control_dir>/library-records/` | 文献状态跟踪（analyze, ocr_status 等） | selection-sync 生成，用户修改状态 |
+| `<system_dir>/PaperForge/exports/` | Better BibTeX JSON 导出 | Zotero 自动导出 |
+| `<system_dir>/PaperForge/ocr/` | OCR 全文 + 图表切割 | ocr worker 生成 |
+| `<system_dir>/Zotero/` | Zotero 数据目录的链接 | 安装时手动创建 junction |
 
 ---
 
@@ -123,23 +123,23 @@ Zotero 添加文献
 ### selection-sync
 - **作用**：检测 Zotero 中的新条目，创建 library-records
 - **运行时机**：添加新文献到 Zotero 后
-- **输出**：`03_Resources/LiteratureControl/library-records/<domain>/<key>.md`
+- **输出**：`<resources_dir>/<control_dir>/library-records/<domain>/<key>.md`
 - **示例**：
   ```bash
-  python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
+  python <system_dir>/PaperForge/worker/scripts/literature_pipeline.py \
     --vault "{vault路径}" selection-sync
   ```
 
 ### index-refresh
 - **作用**：基于 library-records 生成正式文献笔记
 - **运行时机**：selection-sync 之后，或需要更新笔记格式时
-- **输出**：`03_Resources/Literature/<domain>/<key> - <Title>.md`
+- **输出**：`<resources_dir>/<literature_dir>/<domain>/<key> - <Title>.md`
 - **说明**：会读取 Better BibTeX JSON 提取元数据，生成带 frontmatter 的 Obsidian 笔记
 
 ### ocr
 - **作用**：将 PDF 上传到 PaddleOCR API，提取全文文本和图表
 - **触发条件**：library-record 中 `do_ocr: true`
-- **输出**：`99_System/PaperForge/ocr/<key>/` 目录
+- **输出**：`<system_dir>/PaperForge/ocr/<key>/` 目录
   - `fulltext.md`：提取的全文（含 `<!-- page N -->` 分页标记）
   - `images/`：自动切割的图表图片
   - `meta.json`：OCR 状态（`ocr_status: done/pending/processing/failed`）
@@ -198,8 +198,8 @@ year: 2024
 doi: "10.xxxx/xxxxx"
 collection_path: "子分类"        # Zotero 子收藏夹路径
 has_pdf: true                    # 是否有 PDF 附件（自动生成）
-pdf_path: "99_System/Zotero/..." # PDF 相对路径（自动生成）
-fulltext_md_path: "99_System/PaperForge/ocr/..."
+pdf_path: "<system_dir>/Zotero/..." # PDF 相对路径（自动生成）
+fulltext_md_path: "<system_dir>/PaperForge/ocr/..."
 recommend_analyze: true          # 系统推荐精读（有 PDF 时自动设为 true）
 analyze: false                   # 【用户控制】是否生成精读？设为 true 触发
 do_ocr: true                     # 【用户控制】是否运行 OCR？设为 true 触发
@@ -231,7 +231,7 @@ tags:
   - 文献阅读
   - 子分类
 keywords: ["keyword1", "keyword2"]
-pdf_link: "99_System/Zotero/..."
+pdf_link: "<system_dir>/Zotero/..."
 ---
 ```
 
@@ -247,7 +247,7 @@ pdf_link: "99_System/Zotero/..."
 
 ```bash
 # 在 Vault 根目录执行
-python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
+python <system_dir>/PaperForge/worker/scripts/literature_pipeline.py \
   --vault "你的Vault路径" selection-sync
 ```
 
@@ -261,21 +261,21 @@ python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
 ### Step 3: 运行 index-refresh
 
 ```bash
-python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
+python <system_dir>/PaperForge/worker/scripts/literature_pipeline.py \
   --vault "你的Vault路径" index-refresh
 ```
 
 预期输出：
 ```
 [INFO] Generated 5 formal notes
-[INFO] Output: 03_Resources/Literature/骨科/XXXXXXX - Title.md
+[INFO] Output: <resources_dir>/<literature_dir>/骨科/XXXXXXX - Title.md
 ...
 ```
 
 ### Step 4: 标记要精读的文献
 
 在 Obsidian 中：
-1. 打开 `03_Resources/LiteratureControl/library-records/骨科/XXXXXXX.md`
+1. 打开 `<resources_dir>/<control_dir>/library-records/骨科/XXXXXXX.md`
 2. 将 `do_ocr: false` 改为 `do_ocr: true`
 3. 将 `analyze: false` 改为 `analyze: true`
 4. 保存文件
@@ -283,7 +283,7 @@ python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
 ### Step 5: 运行 OCR
 
 ```bash
-python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
+python <system_dir>/PaperForge/worker/scripts/literature_pipeline.py \
   --vault "你的Vault路径" ocr
 ```
 
@@ -292,7 +292,7 @@ python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
 ### Step 6: 检查 OCR 状态
 
 ```bash
-python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
+python <system_dir>/PaperForge/worker/scripts/literature_pipeline.py \
   --vault "你的Vault路径" deep-reading
 ```
 
@@ -324,23 +324,23 @@ Agent 会自动：
 
 ```bash
 # 检测 Zotero 新条目
-python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
+python <system_dir>/PaperForge/worker/scripts/literature_pipeline.py \
   --vault "你的Vault路径" selection-sync
 
 # 生成/更新正式笔记
-python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
+python <system_dir>/PaperForge/worker/scripts/literature_pipeline.py \
   --vault "你的Vault路径" index-refresh
 
 # 运行 OCR（处理 do_ocr=true 的文献）
-python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
+python <system_dir>/PaperForge/worker/scripts/literature_pipeline.py \
   --vault "你的Vault路径" ocr
 
 # 查看精读队列
-python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
+python <system_dir>/PaperForge/worker/scripts/literature_pipeline.py \
   --vault "你的Vault路径" deep-reading
 
 # 查看整体状态
-python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
+python <system_dir>/PaperForge/worker/scripts/literature_pipeline.py \
   --vault "你的Vault路径" status
 ```
 
@@ -362,7 +362,7 @@ python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
 ### Q: OCR 一直显示 pending？
 - 检查 PaddleOCR API Key 是否配置正确（`.env` 文件）
 - 检查网络连接
-- 查看 `99_System/PaperForge/ocr/<key>/meta.json` 中的错误信息
+- 查看 `<system_dir>/PaperForge/ocr/<key>/meta.json` 中的错误信息
 
 ### Q: /LD-deep 提示 OCR 未完成？
 - 确认 library-record 中 `ocr_status: done`
@@ -387,14 +387,17 @@ cd 你的Vault路径
 git pull origin main
 
 # 或手动复制更新文件
-cp -r 新下载的scripts/* 99_System/PaperForge/worker/scripts/
+cp -r 新下载的scripts/* <system_dir>/PaperForge/worker/scripts/
 ```
 
 ### 备份注意事项
-- `03_Resources/` 和 `99_System/PaperForge/ocr/` 包含你的数据，需备份
+- `<resources_dir>/` 和 `<system_dir>/PaperForge/ocr/` 包含你的数据，需备份
 - `.env` 包含 API Key，不要提交到 git
-- `99_System/PaperForge/exports/` 可重新生成（由 Zotero 自动导出）
+- `<system_dir>/PaperForge/exports/` 可重新生成（由 Zotero 自动导出）
 
 ---
 
 *PaperForge Lite | 快速开始指南 | 安装后阅读*
+
+
+

README.md

@@ -58,17 +58,17 @@ python setup_wizard.py --vault /path/to/your/vault
 
 ```
 your-vault/
-├── [资源目录]/                  # 默认: 03_Resources
-│   └── LiteratureControl/
+├── [资源目录]/                  # 安装时可自定义
+│   └── [文献索引目录]/
 │       └── library-records/     # 文献状态跟踪
-├── [系统目录]/                  # 默认: 99_System
+├── [系统目录]/                  # 安装时可自定义
 │   ├── PaperForge/
 │   │   ├── exports/             # Zotero JSON 导出
 │   │   ├── ocr/                 # OCR 结果
 │   │   └── worker/scripts/
 │   │       └── literature_pipeline.py
 │   └── Zotero/                  # Junction 到 Zotero 数据目录
-├── [Agent配置目录]/             # 根据平台: .opencode, .cursor 等
+├── [Agent配置目录]/             # 根据平台和安装配置决定
 │   └── skills/
 │       └── literature-qa/
 │           ├── scripts/ld_deep.py
@@ -89,10 +89,10 @@ your-vault/
 
 ```bash
 # Worker 命令
-python 99_System/PaperForge/worker/scripts/literature_pipeline.py --vault . selection-sync
-python 99_System/PaperForge/worker/scripts/literature_pipeline.py --vault . index-refresh
-python 99_System/PaperForge/worker/scripts/literature_pipeline.py --vault . ocr
-python 99_System/PaperForge/worker/scripts/literature_pipeline.py --vault . status
+python <system_dir>/PaperForge/worker/scripts/literature_pipeline.py --vault . selection-sync
+python <system_dir>/PaperForge/worker/scripts/literature_pipeline.py --vault . index-refresh
+python <system_dir>/PaperForge/worker/scripts/literature_pipeline.py --vault . ocr
+python <system_dir>/PaperForge/worker/scripts/literature_pipeline.py --vault . status
 
 # Agent 命令（在 OpenCode 中使用）
 /LD-deep <zotero_key>    # 完整三阶段精读
@@ -102,3 +102,4 @@ python 99_System/PaperForge/worker/scripts/literature_pipeline.py --vault . stat
 ## License
 
 MIT License — 允许商业使用，需保留版权声明。
+

command/ld-deep.md

@@ -8,9 +8,9 @@
 2. 支持 Zotero key、标题片段、DOI、PMID、关键词
 3. 优先搜索本地 Zotero 并锁定单篇论文
 4. 绑定该论文对应的：
-   - `99_System/PaperForge/ocr/<KEY>/fulltext.md`
-   - `99_System/PaperForge/ocr/<KEY>/meta.json`
-   - `03_Resources/Literature/.../KEY - Title.md`
+   - `<system_dir>/PaperForge/ocr/<KEY>/fulltext.md`
+   - `<system_dir>/PaperForge/ocr/<KEY>/meta.json`
+   - `<resources_dir>/<literature_dir>/.../KEY - Title.md`
 5. 在正式文献卡片中检查或创建 `## 🔍 精读`
 6. 以“研究思路 + figure-by-figure”方式一次性完成精读写回
 
@@ -189,16 +189,16 @@
 | 变量              | 示例值                                                             |
 | ----------------- | ----------------------------------------------------------------- |
 | `{{ZOTERO_KEY}}`   | `Y5KQ4JQ7`                                                        |
-| `{{FORMAL_NOTE}}`  | `D:\L\Med\Research\03_Resources\Literature\骨科\Y5KQ4JQ7 - 3D printed hydrogel for articular cartilage regeneration.md` |
-| `{{FULLTEXT_MD}}`  | `D:\L\Med\Research\99_System\LiteraturePipeline\ocr\Y5KQ4JQ7\fulltext.md` |
-| `{{SCRIPT}}`      | `D:\L\Med\Research\.opencode\skills\literature-qa\scripts\ld_deep.py` |
+| `{{FORMAL_NOTE}}`  | `<Vault>/<resources_dir>/<literature_dir>/骨科/Y5KQ4JQ7 - title.md` |
+| `{{FULLTEXT_MD}}`  | `<Vault>/<system_dir>/PaperForge/ocr/Y5KQ4JQ7/fulltext.md` |
+| `{{SCRIPT}}`      | `<Vault>/<skill_dir>/literature-qa/scripts/ld_deep.py` |
 
 ### Spawn 命令格式
 
 ```
 Task(
   description="LD-deep {{ZOTERO_KEY}}",
-  prompt="加载 subagent prompt: D:\L\Med\Research\.opencode\skills\literature-qa\prompt_deep_subagent.md\n\n填入以下变量：\n- ZOTERO_KEY: {{ZOTERO_KEY}}\n- FORMAL_NOTE: {{FORMAL_NOTE}}\n- FULLTEXT_MD: {{FULLTEXT_MD}}\n- SCRIPT: {{SCRIPT}}",
+  prompt="加载 subagent prompt: <Vault>/<skill_dir>/literature-qa/prompt_deep_subagent.md\n\n填入以下变量：\n- ZOTERO_KEY: {{ZOTERO_KEY}}\n- FORMAL_NOTE: {{FORMAL_NOTE}}\n- FULLTEXT_MD: {{FULLTEXT_MD}}\n- SCRIPT: {{SCRIPT}}",
   subagent_type="general"
 )
 ```

command/ld-paper.md

@@ -7,7 +7,7 @@
 1. 解析 `/LD <query>` 中的查询词
 2. 支持 Zotero key、标题片段、DOI、PMID、关键词
 3. 优先搜索本地 Zotero，解析到单篇目标论文
-4. 加载 `D:\L\Med\Research\99_System\LiteraturePipeline\ocr\<KEY>\fulltext.md` 作为主文本
+4. 根据 Vault 根目录的 `paperforge.json` 加载 `<system_dir>/PaperForge/ocr/<KEY>/fulltext.md` 作为主文本
 5. 读取 `meta.json` 显示论文标题、作者、期刊、年份
 6. 进入 Q&A 模式，用中文回答用户关于该论文的问题
 7. 在当前论文上下文中，用户可再说“精读这篇文章”切换到 deep 层

command/lp-index-refresh.md

@@ -1,16 +1,11 @@
 # /lp-index-refresh
 
-刷新 LiteraturePipeline 索引，包含孤立记录清理逻辑。
+根据 library-records 和 Zotero JSON 导出生成正式文献笔记。
 
-## Commands
+## Command
+
+先读取 Vault 根目录的 `paperforge.json`，用其中的 `system_dir` 拼出 worker 路径，再运行：
 
 ```bash
-python 99_System/PaperForge/worker/scripts/literature_pipeline.py --vault D:\L\Med\Research index-refresh
+python <system_dir>/PaperForge/worker/scripts/literature_pipeline.py --vault . index-refresh
 ```
-
-## 输出示例
-
-```
-index-refresh: wrote 684 index rows
-index-refresh: cleaned 0 orphaned records in 骨科
-```

command/lp-ocr.md

@@ -1,9 +1,11 @@
 # /lp-ocr
 
-触发 OCR 处理队列。
+处理 library-records 中 `do_ocr: true` 的 PDF OCR 队列。
 
-## Commands
+## Command
+
+先读取 Vault 根目录的 `paperforge.json`，用其中的 `system_dir` 拼出 worker 路径，再运行：
 
 ```bash
-python 99_System/PaperForge/worker/scripts/literature_pipeline.py --vault D:\L\Med\Research ocr
-```
+python <system_dir>/PaperForge/worker/scripts/literature_pipeline.py --vault . ocr
+```

command/lp-selection-sync.md

@@ -1,9 +1,11 @@
 # /lp-selection-sync
 
-同步 Zotero 选中项到 library-records。
+同步 Zotero Better BibTeX JSON 导出到 library-records。
 
-## Commands
+## Command
+
+先读取 Vault 根目录的 `paperforge.json`，用其中的 `system_dir` 拼出 worker 路径，再运行：
 
 ```bash
-python 99_System/PaperForge/worker/scripts/literature_pipeline.py --vault D:\L\Med\Research selection-sync
-```
+python <system_dir>/PaperForge/worker/scripts/literature_pipeline.py --vault . selection-sync
+```

command/lp-status.md

@@ -1,27 +1,11 @@
 # /lp-status
 
-查看 LiteraturePipeline 状态。
+查看 PaperForge Lite 当前安装与运行状态。
 
-## 检查 exports 记录数
+## Command
+
+先读取 Vault 根目录的 `paperforge.json`，用其中的 `system_dir` 拼出 worker 路径，再运行：
 
 ```bash
-python -c "import json; from pathlib import Path; data = json.loads(Path('99_System/PaperForge/exports/骨科.json').read_text('utf-8')); items = [i for i in data.get('items',[]) if i.get('itemType') != 'attachment']; print(f'骨科: {len(items)} records')"
+python <system_dir>/PaperForge/worker/scripts/literature_pipeline.py --vault . status
 ```
-
-## 检查 library-records 总数
-
-```bash
-python -c "from pathlib import Path; count = sum(1 for _ in Path('03_Resources/LiteratureControl/library-records').rglob('*.md')); print(f'library-records: {count} records')"
-```
-
-## 检查 OCR 完成数
-
-```bash
-python -c "from pathlib import Path; done = sum(1 for p in Path('99_System/PaperForge/ocr').glob('*/meta.json') if 'done' in Path(p).read_text('utf-8')); print(f'OCR done: {done}')"
-```
-
-## 检查索引记录数
-
-```bash
-python -c "import json; data = json.load(open('99_System/PaperForge/indexes/formal-library.json', encoding='utf-8')); print(f'Index: {len(data)} records')"
-```

docs/INSTALLATION.md

@@ -50,22 +50,22 @@ pip install requests pymupdf pillow
 ### Step 2: 创建目录结构
 
 ```bash
-mkdir -p "{vault_path}/99_System/PaperForge/ocr"
-mkdir -p "{vault_path}/99_System/PaperForge/worker/scripts"
-mkdir -p "{vault_path}/99_System/Zotero"
-mkdir -p "{vault_path}/03_Resources/LiteratureControl/library-records"
+mkdir -p "{vault_path}/<system_dir>/PaperForge/ocr"
+mkdir -p "{vault_path}/<system_dir>/PaperForge/worker/scripts"
+mkdir -p "{vault_path}/<system_dir>/Zotero"
+mkdir -p "{vault_path}/<resources_dir>/<control_dir>/library-records"
 ```
 
 ### Step 3: 链接 Zotero 数据目录
 
 **Windows** (管理员终端):
 ```cmd
-mklink /J "{vault_path}\99_System\Zotero" "C:\Users\<User>\Zotero"
+mklink /J "{vault_path}\<system_dir>\Zotero" "C:\Users\<User>\Zotero"
 ```
 
 **macOS/Linux**:
 ```bash
-ln -s "~/Zotero" "{vault_path}/99_System/Zotero"
+ln -s "~/Zotero" "{vault_path}/<system_dir>/Zotero"
 ```
 
 ### Step 4: 配置 .env
@@ -79,8 +79,8 @@ PADDLEOCR_JOB_URL=https://paddleocr.aistudio-app.com/api/v2/ocr/jobs
 ### Step 5: 部署脚本
 
 ```bash
-cp pipeline/worker/scripts/literature_pipeline.py "{vault_path}/99_System/PaperForge/worker/scripts/"
-cp -r skills/literature-qa "{vault_path}/.opencode/skills/"
+cp pipeline/worker/scripts/literature_pipeline.py "{vault_path}/<system_dir>/PaperForge/worker/scripts/"
+cp -r skills/literature-qa "{vault_path}/<skill_dir>/"
 cp AGENTS.md "{vault_path}/AGENTS.md"
 ```
 
@@ -92,7 +92,7 @@ cp AGENTS.md "{vault_path}/AGENTS.md"
 
 ```bash
 cd "{vault_path}"
-python 99_System/PaperForge/worker/scripts/literature_pipeline.py --vault . status
+python <system_dir>/PaperForge/worker/scripts/literature_pipeline.py --vault . status
 ```
 
 预期输出：
@@ -132,3 +132,4 @@ Status: OK
 5. **开始精读**：使用 `/LD-deep <zotero_key>` 生成结构化阅读笔记
 
 详细用法参见 [AGENTS.md](../AGENTS.md)。
+

docs/setup-guide.md

@@ -90,9 +90,9 @@ Better BibTeX 导出后：
   └── exports/综述.json
 
 PaperForge 自动生成：
-  ├── 05_Bases/骨科.base
-  ├── 05_Bases/运动医学.base
-  └── 05_Bases/综述.base
+  ├── <resources_dir>/<control_dir>/library-records/骨科/
+  ├── <resources_dir>/<control_dir>/library-records/运动医学/
+  └── <resources_dir>/<control_dir>/library-records/综述/
 ```
 
 **规则：一个 JSON 文件 = 一个 Base 视图 = 一个文献分类**
@@ -118,7 +118,7 @@ Zotero
             ├─ 格式(Format): Better BibLaTeX  ★ 重要！不是 BibTeX
             ├─ 勾选 [Keep updated]            ★ 必须勾选
             ├─ 文件名: 骨科.json              ★ 建议用中文名，好识别
-            └─ 保存位置: {你的Vault}/99_System/PaperForge/exports/
+            └─ 保存位置: {你的Vault}/<system_dir>/PaperForge/exports/
                  └─ [保存]
 ```
 
@@ -130,7 +130,7 @@ Zotero
 4. 勾选右下角的 `Keep updated`
 5. 点击 `...` 选择保存位置，导航到：
    ```
-   {你的Vault根目录}/99_System/PaperForge/exports/
+   {你的Vault根目录}/<system_dir>/PaperForge/exports/
    ```
 6. 文件名填写收藏夹名称，如 `骨科.json`
 7. 点击保存
@@ -142,7 +142,7 @@ Zotero
 导出完成后，检查文件：
 
 ```bash
-ls 99_System/PaperForge/exports/
+ls <system_dir>/PaperForge/exports/
 # 应该看到: 骨科.json  运动医学.json  ...
 ```
 
@@ -174,9 +174,9 @@ python pipeline/worker/scripts/literature_pipeline.py --vault . index-refresh
 ```
 
 此时你应该看到：
-- `03_Resources/LiteratureControl/library-records/` 下出现状态记录文件
-- `03_Resources/Literature/` 下出现正式笔记
-- `05_Bases/` 下出现 Base 视图文件（每个 JSON 对应一个）
+- `<resources_dir>/<control_dir>/library-records/` 下出现状态记录文件
+- `<resources_dir>/<literature_dir>/` 下出现正式笔记
+- `<resources_dir>/<control_dir>/library-records/` 下出现状态记录文件
 
 ---
 
@@ -222,3 +222,6 @@ python setup_wizard.py --vault .
 ---
 
 *PaperForge Lite | 安装指南*
+
+
+

paperforge.json

@@ -9,12 +9,12 @@
     "check_interval_days": 7
   },
   "protected_paths": [
-    "03_Resources/",
-    "05_Bases/",
-    "99_System/PaperForge/ocr/",
-    "99_System/PaperForge/exports/",
-    "99_System/PaperForge/indexes/",
-    "99_System/PaperForge/candidates/",
+    "<resources_dir>/",
+    "<base_dir>/",
+    "<system_dir>/PaperForge/ocr/",
+    "<system_dir>/PaperForge/exports/",
+    "<system_dir>/PaperForge/indexes/",
+    "<system_dir>/PaperForge/candidates/",
     ".env",
     "AGENTS.md"
   ],
@@ -26,3 +26,6 @@
   ],
   "changelog_url": "https://github.com/LLLin000/PaperForge/releases"
 }
+
+
+

pipeline/worker/scripts/literature_pipeline.py

@@ -45,7 +45,7 @@ def load_journal_db(vault: Path) -> dict[str, dict]:
     global _JOURNAL_DB
     if _JOURNAL_DB is not None:
         return _JOURNAL_DB
-    zoterostyle_path = vault / '99_System' / 'Zotero' / 'zoterostyle.json'
+    zoterostyle_path = vault / load_vault_config(vault)['system_dir'] / 'Zotero' / 'zoterostyle.json'
     if zoterostyle_path.exists():
         try:
             _JOURNAL_DB = read_json(zoterostyle_path)
@@ -125,27 +125,41 @@ def _extract_year(value: str) -> str:
 
 def load_vault_config(vault: Path) -> dict:
     """Read vault configuration from paperforge.json."""
+    defaults = {
+        "system_dir": "99_System",
+        "resources_dir": "03_Resources",
+        "literature_dir": "Literature",
+        "control_dir": "LiteratureControl",
+        "base_dir": "05_Bases",
+    }
     pf_json = vault / "paperforge.json"
     if pf_json.exists():
         try:
             data = json.loads(pf_json.read_text(encoding="utf-8"))
+            nested = data.get("vault_config", {}) if isinstance(data.get("vault_config"), dict) else {}
+            merged = {**defaults, **nested, **{k: v for k, v in data.items() if k in defaults and v}}
             return {
-                "system_dir": data.get("system_dir", "99_System"),
-                "resources_dir": data.get("resources_dir", "03_Resources"),
-                "literature_dir": data.get("literature_dir", "Literature"),
+                "system_dir": merged["system_dir"],
+                "resources_dir": merged["resources_dir"],
+                "literature_dir": merged["literature_dir"],
+                "control_dir": merged["control_dir"],
+                "base_dir": merged["base_dir"],
             }
         except (json.JSONDecodeError, IOError):
             pass
-    return {"system_dir": "99_System", "resources_dir": "03_Resources", "literature_dir": "Literature"}
+    return defaults
 
 
 def pipeline_paths(vault: Path) -> dict[str, Path]:
     cfg = load_vault_config(vault)
     system_dir = cfg["system_dir"]
     resources_dir = cfg["resources_dir"]
+    literature_dir = cfg["literature_dir"]
+    control_dir = cfg["control_dir"]
+    base_dir = cfg["base_dir"]
     
     root = vault / system_dir / "PaperForge"
-    control_root = vault / resources_dir / "LiteratureControl"
+    control_root = vault / resources_dir / control_dir
     return {
         'pipeline': root,
         'candidates': root / 'candidates' / 'candidates.json',
@@ -168,8 +182,88 @@ def pipeline_paths(vault: Path) -> dict[str, Path]:
         'ocr': root / 'ocr',
         'ocr_queue': root / 'ocr' / 'ocr-queue.json',
         'resources': vault / resources_dir,
+        'literature': vault / resources_dir / literature_dir,
+        'bases': vault / base_dir,
     }
 
+def load_domain_config(paths: dict[str, Path]) -> dict:
+    """Load or create the Lite domain mapping from export JSON files."""
+    config_path = paths['config']
+    if config_path.exists():
+        config = read_json(config_path)
+    else:
+        config = {"domains": []}
+    domains = config.setdefault("domains", [])
+    known_exports = {str(entry.get("export_file", "")) for entry in domains}
+    changed = not config_path.exists()
+    for export_path in sorted(paths['exports'].glob('*.json')):
+        if export_path.name in known_exports:
+            continue
+        domains.append({"domain": export_path.stem, "export_file": export_path.name, "allowed_collections": []})
+        known_exports.add(export_path.name)
+        changed = True
+    if changed:
+        config_path.parent.mkdir(parents=True, exist_ok=True)
+        write_json(config_path, config)
+    return config
+
+def base_markdown_filter(path: Path, vault: Path) -> str:
+    try:
+        return str(path.relative_to(vault)).replace('\\', '/')
+    except ValueError:
+        return str(path).replace('\\', '/')
+
+def write_base_file(path: Path, folder_filter: str, name: str) -> None:
+    path.parent.mkdir(parents=True, exist_ok=True)
+    content = f"""filters:
+  and:
+    - file.inFolder("{folder_filter}")
+properties:
+  zotero_key:
+    displayName: "Zotero Key"
+  title:
+    displayName: "Title"
+  year:
+    displayName: "Year"
+  has_pdf:
+    displayName: "PDF"
+  do_ocr:
+    displayName: "OCR"
+  analyze:
+    displayName: "Analyze"
+  ocr_status:
+    displayName: "OCR Status"
+  deep_reading_status:
+    displayName: "Deep Reading"
+views:
+  - type: table
+    name: "{name}"
+    order:
+      - file.name
+      - title
+      - year
+      - has_pdf
+      - do_ocr
+      - analyze
+      - ocr_status
+      - deep_reading_status
+      - pdf_path
+      - fulltext_md_path
+"""
+    path.write_text(content, encoding='utf-8')
+
+def ensure_base_views(vault: Path, paths: dict[str, Path], config: dict) -> None:
+    paths['bases'].mkdir(parents=True, exist_ok=True)
+    records_root = paths['library_records']
+    write_base_file(paths['bases'] / 'PaperForge.base', base_markdown_filter(records_root, vault), 'All Records')
+    seen_domains = set()
+    for entry in config.get('domains', []):
+        domain = str(entry.get('domain', '') or '').strip()
+        if not domain or domain in seen_domains:
+            continue
+        seen_domains.add(domain)
+        write_base_file(paths['bases'] / f"{slugify_filename(domain)}.base", base_markdown_filter(records_root / domain, vault), domain)
+
 def build_collection_lookup(collections: dict) -> dict:
     path_cache = {}
     item_paths = {}
@@ -596,7 +690,8 @@ def load_control_actions(paths: dict[str, Path]) -> dict[str, dict]:
 
 def run_selection_sync(vault: Path) -> int:
     paths = pipeline_paths(vault)
-    config = read_json(paths['config'])
+    config = load_domain_config(paths)
+    ensure_base_views(vault, paths, config)
     domain_lookup = {entry['export_file']: entry['domain'] for entry in config['domains']}
     written = 0
     updated = 0
@@ -617,7 +712,7 @@ def run_selection_sync(vault: Path) -> int:
                 if validated_error:
                     meta['error'] = validated_error
                     write_json(meta_path, meta)
-            note_path = paths['resources'] / 'Literature' / domain / f"{item['key']} - {slugify_filename(item['title'])}.md"
+            note_path = paths['literature'] / domain / f"{item['key']} - {slugify_filename(item['title'])}.md"
             note_text = note_path.read_text(encoding='utf-8') if note_path.exists() else ''
             fulltext_md_path = obsidian_wikilink_for_path(vault, meta.get('fulltext_md_path', '') or meta.get('markdown_path', ''))
             ocr_status = meta.get('ocr_status', 'pending')
@@ -1119,7 +1214,8 @@ def analyze_selected_keys(paths: dict[str, Path]) -> set[str]:
 
 def run_index_refresh(vault: Path) -> int:
     paths = pipeline_paths(vault)
-    config = read_json(paths['config'])
+    config = load_domain_config(paths)
+    ensure_base_views(vault, paths, config)
     domain_lookup = {entry['export_file']: entry['domain'] for entry in config['domains']}
     exports = {}
     for export_path in sorted(paths['exports'].glob('*.json')):
@@ -1128,7 +1224,7 @@ def run_index_refresh(vault: Path) -> int:
         exports[domain] = {row['key']: row for row in export_rows}
     selected_keys = None
     index_rows = []
-    lit_root = paths['resources'] / 'Literature'
+    lit_root = paths['literature']
     for export_path in sorted(paths['exports'].glob('*.json')):
         domain = domain_lookup.get(export_path.name, export_path.stem)
         export_rows = load_export_rows(export_path)
@@ -1159,7 +1255,7 @@ def run_index_refresh(vault: Path) -> int:
             index_rows.append(entry)
     write_json(paths['index'], index_rows)
     print(f'index-refresh: wrote {len(index_rows)} index rows')
-    control_records_dir = paths['resources'] / 'LiteratureControl' / 'library-records'
+    control_records_dir = paths['library_records']
     if control_records_dir.exists():
         for domain_dir in control_records_dir.iterdir():
             if not domain_dir.is_dir():
@@ -1218,7 +1314,11 @@ def ensure_ocr_meta(vault: Path, row: dict) -> dict:
     meta.setdefault('page_count', 0)
     meta.setdefault('markdown_path', '')
     meta.setdefault('json_path', '')
-    meta.setdefault('assets_path', f'99_System/PaperForge/ocr/{key}/images')
+    try:
+        assets_path = str((paths['ocr'] / key / 'images').relative_to(vault)).replace('\\', '/')
+    except ValueError:
+        assets_path = str(paths['ocr'] / key / 'images')
+    meta.setdefault('assets_path', assets_path)
     meta.setdefault('fulltext_md_path', '')
     meta.setdefault('error', '')
     return meta
@@ -2314,9 +2414,17 @@ def run_ocr(vault: Path) -> int:
                 write_json(paths['ocr'] / key / 'meta.json', meta)
                 changed += 1
                 continue
-            with open(queue_row['pdf_path'], 'rb') as file_handle:
-                response = requests.post(job_url, headers={'Authorization': f'bearer {token}'}, data={'model': model, 'optionalPayload': json.dumps(optional_payload)}, files={'file': file_handle}, timeout=120)
-            response.raise_for_status()
+            try:
+                with open(queue_row['pdf_path'], 'rb') as file_handle:
+                    response = requests.post(job_url, headers={'Authorization': f'bearer {token}'}, data={'model': model, 'optionalPayload': json.dumps(optional_payload)}, files={'file': file_handle}, timeout=120)
+                response.raise_for_status()
+            except requests.RequestException as e:
+                meta['ocr_status'] = 'error'
+                meta['error'] = f'PaddleOCR request failed: {e}'
+                queue_row['queue_status'] = 'error'
+                write_json(paths['ocr'] / key / 'meta.json', meta)
+                changed += 1
+                continue
             meta['ocr_job_id'] = response.json()['data']['jobId']
             meta['ocr_status'] = 'queued'
             meta['ocr_started_at'] = datetime.now(timezone.utc).isoformat()
@@ -2334,8 +2442,8 @@ def run_ocr(vault: Path) -> int:
     return 0
 
 def _resolve_formal_note_path(vault: Path, zotero_key: str, domain: str) -> Path | None:
-    """Resolve formal literature note from 03_Resources/Literature by zotero_key."""
-    lit_root = vault / '03_Resources' / 'Literature'
+    """Resolve formal literature note by zotero_key."""
+    lit_root = pipeline_paths(vault)['literature']
     domain_dir = lit_root / domain
     if not domain_dir.exists():
         return None
@@ -2360,7 +2468,8 @@ def run_deep_reading(vault: Path) -> int:
     Actual content filling is done via /LD-deep (agent-driven).
     """
     paths = pipeline_paths(vault)
-    config = read_json(paths['config'])
+    config = load_domain_config(paths)
+    ensure_base_views(vault, paths, config)
     domain_lookup = {entry['export_file']: entry['domain'] for entry in config['domains']}
     synced = 0
     pending_queue: list[dict] = []
@@ -2419,6 +2528,45 @@ def run_deep_reading(vault: Path) -> int:
     print(f'deep-reading: synced {synced} records, {len(pending_queue)} pending')
     return 0
 
+def run_status(vault: Path) -> int:
+    """Print a compact Lite install/runtime status."""
+    paths = pipeline_paths(vault)
+    cfg = load_vault_config(vault)
+    config = load_domain_config(paths)
+    ensure_base_views(vault, paths, config)
+    export_files = sorted(paths['exports'].glob('*.json'))
+    record_count = sum(1 for _ in paths['library_records'].rglob('*.md')) if paths['library_records'].exists() else 0
+    note_count = sum(1 for _ in paths['literature'].rglob('*.md')) if paths['literature'].exists() else 0
+    base_count = sum(1 for _ in paths['bases'].glob('*.base')) if paths['bases'].exists() else 0
+    ocr_done = 0
+    ocr_total = 0
+    if paths['ocr'].exists():
+        for meta_path in paths['ocr'].glob('*/meta.json'):
+            ocr_total += 1
+            try:
+                meta = read_json(meta_path)
+            except Exception:
+                continue
+            if str(meta.get('ocr_status', '')).strip().lower() == 'done':
+                ocr_done += 1
+    env_paths = [vault / '.env', paths['pipeline'] / '.env']
+    env_found = [str(path.relative_to(vault)).replace('\\', '/') for path in env_paths if path.exists()]
+
+    print('PaperForge Lite status')
+    print(f"- vault: {vault}")
+    print(f"- system_dir: {cfg['system_dir']}")
+    print(f"- resources_dir: {cfg['resources_dir']}")
+    print(f"- literature_dir: {cfg['literature_dir']}")
+    print(f"- control_dir: {cfg['control_dir']}")
+    print(f"- exports: {len(export_files)} JSON file(s)")
+    print(f"- domains: {len(config.get('domains', []))}")
+    print(f"- library_records: {record_count}")
+    print(f"- formal_notes: {note_count}")
+    print(f"- bases: {base_count}")
+    print(f"- ocr: {ocr_done}/{ocr_total} done")
+    print(f"- env: {', '.join(env_found) if env_found else 'not configured'}")
+    return 0
+
 # =============================================================================
 # Update 功能
 # =============================================================================
@@ -2426,17 +2574,24 @@ def run_deep_reading(vault: Path) -> int:
 GITHUB_REPO = "LLLin000/PaperForge"
 GITHUB_ZIP = f"https://github.com/{GITHUB_REPO}/archive/refs/heads/master.zip"
 
-PROTECTED_PATHS = {
-    "03_Resources", "05_Bases",
-    "99_System/PaperForge/ocr",
-    "99_System/PaperForge/exports",
-    "99_System/PaperForge/indexes",
-    "99_System/PaperForge/candidates",
-    ".env", "AGENTS.md",
-}
 UPDATEABLE_PATHS = ["skills", "pipeline", "command", "scripts"]
 
 
+def protected_paths(vault: Path) -> set[str]:
+    cfg = load_vault_config(vault)
+    pf = f"{cfg['system_dir']}/PaperForge"
+    return {
+        cfg["resources_dir"],
+        cfg["base_dir"],
+        f"{pf}/ocr",
+        f"{pf}/exports",
+        f"{pf}/indexes",
+        f"{pf}/candidates",
+        ".env",
+        "AGENTS.md",
+    }
+
+
 def _color(text: str, c: str = "") -> str:
     colors = {"r": "\033[91m", "g": "\033[92m", "y": "\033[93m", "b": "\033[94m", "c": "\033[96m", "x": "\033[0m"}
     if sys.platform == "win32" and not os.environ.get("FORCE_COLOR"):
@@ -2463,6 +2618,7 @@ def _remote_version() -> str | None:
 
 def _scan_updates(vault: Path, source: Path) -> list[tuple[Path, Path, str]]:
     updates = []
+    protected = protected_paths(vault)
     for name in UPDATEABLE_PATHS:
         src_dir = source / name
         if not src_dir.exists():
@@ -2473,7 +2629,7 @@ def _scan_updates(vault: Path, source: Path) -> list[tuple[Path, Path, str]]:
             rel = src.relative_to(source)
             dst = vault / rel
             rel_str = str(rel).replace("\\", "/")
-            if any(rel_str.startswith(p) for p in PROTECTED_PATHS):
+            if any(rel_str.startswith(p) for p in protected):
                 continue
             if dst.exists():
                 if hashlib.sha256(src.read_bytes()).hexdigest() != hashlib.sha256(dst.read_bytes()).hexdigest():
@@ -2628,11 +2784,12 @@ def main() -> int:
     parser.add_argument('--limit', type=int, default=8)
     parser.add_argument('--sources', nargs='+')
     parser.add_argument('--skip-ingest', action='store_true')
-    parser.add_argument('worker', choices=['selection-sync', 'index-refresh', 'ocr', 'deep-reading', 'update', 'wizard', 'all'])
+    parser.add_argument('worker', choices=['selection-sync', 'index-refresh', 'ocr', 'deep-reading', 'status', 'update', 'wizard', 'all'])
     args = parser.parse_args()
-    # Load .env from vault root first, then from PaperForge directory
+    paths = pipeline_paths(args.vault)
+    # Load .env from vault root first, then from the configured PaperForge directory.
     load_simple_env(args.vault / '.env')
-    load_simple_env(args.vault / '99_System' / 'PaperForge' / '.env')
+    load_simple_env(paths['pipeline'] / '.env')
     if args.worker == 'selection-sync':
         return run_selection_sync(args.vault)
     if args.worker == 'index-refresh':
@@ -2641,6 +2798,8 @@ def main() -> int:
         return run_ocr(args.vault)
     if args.worker == 'deep-reading':
         return run_deep_reading(args.vault)
+    if args.worker == 'status':
+        return run_status(args.vault)
     if args.worker == 'update':
         return run_update(args.vault)
     if args.worker == 'wizard':
@@ -2661,4 +2820,4 @@ def main() -> int:
         return code
     return run_deep_reading(args.vault)
 if __name__ == '__main__':
-    raise SystemExit(main())
+    raise SystemExit(main())

scripts/validate_setup.py

@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
-"""Validate literature workflow setup."""
+"""Validate a PaperForge Lite installation."""
 
 from __future__ import annotations
 
@@ -9,220 +9,108 @@ import sys
 from pathlib import Path
 
 
-def check_path(label: str, path: str | Path, expected_type: str = "file") -> tuple[bool, str]:
-    """Check if a path exists and is the expected type."""
-    p = Path(path)
-    if not p.exists():
+def check_path(label: str, path: Path, expected_type: str = "file") -> tuple[bool, str]:
+    if not path.exists():
         return False, f"[FAIL] {label}: not found at {path}"
-    
-    if expected_type == "file" and not p.is_file():
+    if expected_type == "file" and not path.is_file():
         return False, f"[FAIL] {label}: exists but is not a file ({path})"
-    if expected_type == "dir" and not p.is_dir():
+    if expected_type == "dir" and not path.is_dir():
         return False, f"[FAIL] {label}: exists but is not a directory ({path})"
-    
     return True, f"[OK] {label}: {path}"
 
 
-def validate_zotero(zotero_path: str) -> list[tuple[bool, str]]:
-    """Validate Zotero installation and data directory."""
-    results = []
-    zotero_dir = Path(zotero_path)
-    
-    # Check main directory
-    ok, msg = check_path("Zotero data directory", zotero_path, "dir")
-    results.append((ok, msg))
-    if not ok:
-        return results
-    
-    # Check zotero.sqlite
-    sqlite_path = zotero_dir / "zotero.sqlite"
-    ok, msg = check_path("zotero.sqlite", sqlite_path, "file")
-    results.append((ok, msg))
-    
-    # Check better-bibtex JSON (optional but recommended)
-    bbt_path = zotero_dir / "better-bibtex.json"
-    if bbt_path.exists():
-        results.append((True, f"[OK] Better BibTeX config: {bbt_path}"))
-    else:
-        results.append((False, f"[WARN] Better BibTeX config not found (optional but recommended): {bbt_path}"))
-    
-    return results
-
-
-def validate_obsidian(vault_path: str) -> list[tuple[bool, str]]:
-    """Validate Obsidian vault structure."""
-    results = []
-    vault_dir = Path(vault_path)
-    
-    ok, msg = check_path("Obsidian vault", vault_path, "dir")
-    results.append((ok, msg))
-    if not ok:
-        return results
-    
-    # Check expected subdirectories
-    expected_dirs = [
-        "00_Inbox",
-        "01_Projects", 
-        "02_Areas",
-        "03_Resources",
-        "04_Archives",
-        "05_Bases",
-        "99_System",
-    ]
-    
-    for subdir in expected_dirs:
-        subpath = vault_dir / subdir
-        ok, msg = check_path(f"Vault subdirectory: {subdir}", subpath, "dir")
-        results.append((ok, msg))
-    
-    return results
-
-
-def validate_ocr_pipeline(vault_path: str) -> list[tuple[bool, str]]:
-    """Validate OCR pipeline configuration."""
-    results = []
-    vault_dir = Path(vault_path)
-    
-    # Check .env file
-    env_path = vault_dir / ".env"
-    ok, msg = check_path("Environment config (.env)", env_path, "file")
-    results.append((ok, msg))
-    
-    if ok:
-        # Check if PADDLEOCR_API_TOKEN is set
-        env_content = env_path.read_text(encoding='utf-8')
-        if "PADDLEOCR_API_TOKEN" in env_content:
-            results.append((True, "[OK] PADDLEOCR_API_TOKEN configured in .env"))
-        else:
-            results.append((False, "[FAIL] PADDLEOCR_API_TOKEN not found in .env"))
-    
-    # Check OCR pipeline directory
-    ocr_dir = vault_dir / "99_System" / "LiteraturePipeline" / "worker"
-    ok, msg = check_path("OCR pipeline directory", ocr_dir, "dir")
-    results.append((ok, msg))
-    
-    # Check worker script
-    worker_path = ocr_dir / "scripts" / "literature_pipeline.py"
-    ok, msg = check_path("OCR worker script", worker_path, "file")
-    results.append((ok, msg))
-    
-    return results
-
-
-def validate_ld_deep(vault_path: str) -> list[tuple[bool, str]]:
-    """Validate /LD-deep command setup."""
-    results = []
-    vault_dir = Path(vault_path)
-    
-    # Check ld_deep.py script
-    ld_deep_path = vault_dir / ".opencode" / "skills" / "literature-qa" / "scripts" / "ld_deep.py"
-    ok, msg = check_path("LD-deep script", ld_deep_path, "file")
-    results.append((ok, msg))
-    
-    # Check prompt
-    prompt_path = vault_dir / ".opencode" / "skills" / "literature-qa" / "prompt_deep_subagent.md"
-    ok, msg = check_path("LD-deep subagent prompt", prompt_path, "file")
-    results.append((ok, msg))
-    
-    # Check chart reading guides
-    
-    
-    if ok:
-        # Count guide files
-        guide_files = list(chart_guide_dir.glob("*.md"))
-        if len(guide_files) >= 14:
-            results.append((True, f"[OK] Found {len(guide_files)} chart reading guides"))
-        else:
-            results.append((False, f"[WARN] Only {len(guide_files)} chart guides found (expected 14+)"))
-    
-    return results
+def load_config(vault: Path) -> dict:
+    defaults = {
+        "system_dir": "99_System",
+        "resources_dir": "03_Resources",
+        "literature_dir": "Literature",
+        "control_dir": "LiteratureControl",
+        "base_dir": "05_Bases",
+        "skill_dir": ".opencode/skills",
+    }
+    config_path = vault / "paperforge.json"
+    if not config_path.exists():
+        return defaults
+    try:
+        data = json.loads(config_path.read_text(encoding="utf-8"))
+    except Exception:
+        return defaults
+    nested = data.get("vault_config", {}) if isinstance(data.get("vault_config"), dict) else {}
+    return {**defaults, **nested, **{k: v for k, v in data.items() if k in defaults and v}}
 
 
 def validate_python_deps() -> list[tuple[bool, str]]:
-    """Check Python dependencies."""
     results = []
-    required = {
-        "requests": "requests",
-        "pymupdf": "fitz",
-        "pillow": "PIL",
-        "pytest": "pytest",
-    }
-    
+    required = {"requests": "requests", "pymupdf": "fitz", "pillow": "PIL", "textual": "textual"}
     for package, import_name in required.items():
         try:
             __import__(import_name)
             results.append((True, f"[OK] Python package installed: {package}"))
         except ImportError:
-            results.append((False, f"[FAIL] Python package missing: {package} (pip install {package})"))
-    
+            results.append((False, f"[FAIL] Python package missing: {package}"))
     return results
 
 
-def main():
-    """Run all validation checks."""
-    print("=" * 60)
-    print("Literature Workflow Setup Validation")
-    print("=" * 60)
-    
-    # Load config from .env or config.json
-    vault_path = os.environ.get("VAULT_PATH", ".")
-    zotero_path = os.environ.get("ZOTERO_PATH", "")
-    
-    config_path = Path(vault_path) / "config.json"
-    if config_path.exists():
-        config = json.loads(config_path.read_text(encoding="utf-8"))
-        vault_path = config.get("vault_path", vault_path)
-        zotero_path = config.get("zotero_path", zotero_path)
-    
+def validate_vault(vault: Path, cfg: dict) -> list[tuple[bool, str]]:
+    results = [check_path("Obsidian vault", vault, "dir")]
+    if not results[0][0]:
+        return results
+    pf_root = vault / cfg["system_dir"] / "PaperForge"
+    control_root = vault / cfg["resources_dir"] / cfg["control_dir"] / "library-records"
+    literature_root = vault / cfg["resources_dir"] / cfg["literature_dir"]
+    base_root = vault / cfg["base_dir"]
+    for label, path, kind in [
+        ("paperforge.json", vault / "paperforge.json", "file"),
+        ("PaperForge root", pf_root, "dir"),
+        ("exports directory", pf_root / "exports", "dir"),
+        ("ocr directory", pf_root / "ocr", "dir"),
+        ("domain config", pf_root / "config" / "domain-collections.json", "file"),
+        ("worker script", pf_root / "worker" / "scripts" / "literature_pipeline.py", "file"),
+        ("library records directory", control_root, "dir"),
+        ("literature notes directory", literature_root, "dir"),
+        ("Base directory", base_root, "dir"),
+    ]:
+        results.append(check_path(label, path, kind))
+    env_path = pf_root / ".env"
+    ok, msg = check_path("PaperForge .env", env_path, "file")
+    results.append((ok, msg))
+    if ok:
+        env_text = env_path.read_text(encoding="utf-8")
+        for key in ("PADDLEOCR_API_TOKEN", "PADDLEOCR_JOB_URL"):
+            results.append((key in env_text, f"[{'OK' if key in env_text else 'FAIL'}] {key} configured"))
+    return results
+
+
+def validate_agent(vault: Path, cfg: dict) -> list[tuple[bool, str]]:
+    skill_root = vault / cfg["skill_dir"] / "literature-qa"
+    results = [
+        check_path("LD-deep script", skill_root / "scripts" / "ld_deep.py", "file"),
+        check_path("LD-deep subagent prompt", skill_root / "prompt_deep_subagent.md", "file"),
+        check_path("chart-reading directory", skill_root / "chart-reading", "dir"),
+    ]
+    chart_dir = skill_root / "chart-reading"
+    if chart_dir.exists():
+        guide_count = len(list(chart_dir.glob("*.md")))
+        results.append((guide_count >= 14, f"[{'OK' if guide_count >= 14 else 'WARN'}] chart-reading guides: {guide_count}"))
+    return results
+
+
+def main() -> int:
+    vault = Path(os.environ.get("VAULT_PATH", ".")).resolve()
+    cfg = load_config(vault)
     all_results = []
-    
-    # Python dependencies
-    print("\n## Python Dependencies")
     all_results.extend(validate_python_deps())
-    
-    # Zotero
-    if zotero_path:
-        print("\n## Zotero Integration")
-        all_results.extend(validate_zotero(zotero_path))
-    else:
-        all_results.append((False, "[SKIP] Zotero path not configured"))
-    
-    # Obsidian vault
-    print("\n## Obsidian Vault")
-    all_results.extend(validate_obsidian(vault_path))
-    
-    # OCR pipeline
-    print("\n## OCR Pipeline")
-    all_results.extend(validate_ocr_pipeline(vault_path))
-    
-    # LD-deep
-    print("\n## LD-deep Commands")
-    all_results.extend(validate_ld_deep(vault_path))
-    
-    # Summary
-    print("\n" + "=" * 60)
+    all_results.extend(validate_vault(vault, cfg))
+    all_results.extend(validate_agent(vault, cfg))
+
     passed = sum(1 for ok, _ in all_results if ok)
-    failed = sum(1 for ok, _ in all_results if not ok)
-    warnings = sum(1 for ok, msg in all_results if not ok and msg.startswith("[WARN]"))
-    
-    print(f"Results: {passed} passed, {failed} failed ({warnings} warnings)")
-    print("=" * 60)
-    
-    # Print failures
-    failures = [msg for ok, msg in all_results if not ok and not msg.startswith("[WARN]")]
-    if failures:
-        print("\n### Failures to fix:")
-        for msg in failures:
-            print(f"  - {msg}")
-    
-    warnings_list = [msg for ok, msg in all_results if not ok and msg.startswith("[WARN]")]
-    if warnings_list:
-        print("\n### Warnings (optional):")
-        for msg in warnings_list:
-            print(f"  - {msg}")
-    
-    return 0 if not failures else 1
+    failed = [msg for ok, msg in all_results if not ok and not msg.startswith("[WARN]")]
+    warnings = [msg for ok, msg in all_results if not ok and msg.startswith("[WARN]")]
+    print(f"PaperForge Lite validation: {passed} passed, {len(failed)} failed, {len(warnings)} warnings")
+    for _, msg in all_results:
+        print(msg)
+    return 0 if not failed else 1
 
 
 if __name__ == "__main__":
-    sys.exit(main())
+    raise SystemExit(main())

setup_wizard.py

@@ -16,10 +16,14 @@ import platform
 import subprocess
 import sys
 import webbrowser
-import winreg
 from pathlib import Path
 from typing import Optional
 
+if sys.platform == "win32":
+    import winreg
+else:
+    winreg = None
+
 from textual.app import App, ComposeResult
 from textual.containers import Container, Grid, Horizontal, Vertical
 from textual.message import Message
@@ -43,7 +47,7 @@ from textual.widgets import (
 # =============================================================================
 
 AGENT_CONFIGS = {
-    "opencode": {"name": "OpenCode", "skill_dir": ".opencode/skills", "config_file": None},
+    "opencode": {"name": "OpenCode", "skill_dir": ".opencode/skills", "command_dir": ".opencode/command", "config_file": None},
     "cursor": {"name": "Cursor", "skill_dir": ".cursor/skills", "config_file": ".cursor/settings.json"},
     "claude": {"name": "Claude Code", "skill_dir": ".claude/skills", "config_file": ".claude/skills.json"},
     "windsurf": {"name": "Windsurf", "skill_dir": ".windsurf/skills", "config_file": None},
@@ -370,7 +374,7 @@ class WelcomeStep(StepScreen):
 
     def compose(self) -> ComposeResult:
         yield from super().compose()
-        yield Static("""
+        yield Static(r"""
     ______  ___  ______ _________________ ___________ _____  _____ 
     | ___ \/ _ \ | ___ \  ___| ___ \  ___|  _  | ___ \  __ \|  ___|
     | |_/ / /_\ \| |_/ / |__ | |_/ / |_  | | | | |_/ / |  \/| |__  
@@ -516,6 +520,8 @@ Obsidian Vault/
         yield Input(value="Literature", id="input-literature-dir")
         yield Static("文献索引文件夹名称:", classes="step-title")
         yield Input(value="LiteratureControl", id="input-control-dir")
+        yield Static("Obsidian Base 文件夹名称:", classes="step-title")
+        yield Input(value="05_Bases", id="input-base-dir")
         yield Horizontal(
             Button("✓ 确认并创建目录", id="btn-setup-vault", variant="primary"),
             id="btn-row",
@@ -545,6 +551,7 @@ Obsidian Vault/
             resources_dir = self.query_one("#input-resources-dir", Input).value.strip() or "03_Resources"
             literature_dir = self.query_one("#input-literature-dir", Input).value.strip() or "Literature"
             control_dir = self.query_one("#input-control-dir", Input).value.strip() or "LiteratureControl"
+            base_dir = self.query_one("#input-base-dir", Input).value.strip() or "05_Bases"
 
             # 解析路径（支持名称、相对路径、绝对路径）
             def resolve_path(base: Path, path_str: str) -> Path:
@@ -556,6 +563,7 @@ Obsidian Vault/
 
             system_path = resolve_path(vault_path, system_dir)
             resources_path = resolve_path(vault_path, resources_dir)
+            base_path = resolve_path(vault_path, base_dir)
 
             # 保存配置
             self.app.vault_config = {
@@ -564,13 +572,16 @@ Obsidian Vault/
                 "resources_dir": resources_dir,
                 "literature_dir": literature_dir,
                 "control_dir": control_dir,
+                "base_dir": base_dir,
                 "paperforge_path": str(system_path / "PaperForge"),
                 "literature_path": str(resources_path / literature_dir),
+                "base_path": str(base_path),
             }
 
             # 创建目录
             dirs_to_create = [
                 resources_path / control_dir / "library-records",
+                base_path,
                 system_path / "PaperForge" / "exports",
                 system_path / "PaperForge" / "ocr",
             ]
@@ -671,6 +682,7 @@ class ZoteroStep(StepScreen):
             
             if is_inside_vault:
                 # 在 Vault 内部，直接通过
+                self.app.zotero_data_dir = str(zotero_data)
                 self.set_status("Zotero 数据目录已确认", True)
                 self.app.post_message(StepPassed(self.step_idx))
                 return
@@ -698,6 +710,8 @@ class ZoteroStep(StepScreen):
                     )
                 else:
                     junction_path.symlink_to(zotero_data, target_is_directory=True)
+                self.app.zotero_data_dir = str(zotero_data)
+                self.app.zotero_link = str(junction_path)
                 self.set_status("链接已创建", True)
                 self.app.post_message(StepPassed(self.step_idx))
             except Exception as e:
@@ -818,8 +832,8 @@ class DeployStep(StepScreen):
         yield Input(placeholder="粘贴你的 PaddleOCR API Key", id="input-api-key")
         yield Static("PaddleOCR API URL:", classes="step-title")
         yield Input(
-            value="https://api.paddleocr.com/ocr",
-            placeholder="https://api.paddleocr.com/ocr",
+            value="https://paddleocr.aistudio-app.com/api/v2/ocr/jobs",
+            placeholder="https://paddleocr.aistudio-app.com/api/v2/ocr/jobs",
             id="input-api-url",
         )
         yield Horizontal(
@@ -866,6 +880,34 @@ class DeployStep(StepScreen):
         vault_config = getattr(self.app, 'vault_config', {})
         system_dir = vault_config.get('system_dir', '99_System')
         resources_dir = vault_config.get('resources_dir', '03_Resources')
+        literature_dir = vault_config.get('literature_dir', 'Literature')
+        control_dir = vault_config.get('control_dir', 'LiteratureControl')
+        base_dir = vault_config.get('base_dir', '05_Bases')
+
+        def apply_user_paths(text: str, skill_dir_value: str = "") -> str:
+            agent_config_dir = str(Path(skill_dir_value or ".opencode/skills").parent).replace("\\", "/")
+            replacements = {
+                "<system_dir>": system_dir,
+                "<resources_dir>": resources_dir,
+                "<literature_dir>": literature_dir,
+                "<control_dir>": control_dir,
+                "<base_dir>": base_dir,
+                "<skill_dir>": skill_dir_value,
+                "<agent_config_dir>": agent_config_dir,
+                "99_System/PaperForge": f"{system_dir}/PaperForge",
+                "99_System\\PaperForge": f"{system_dir}\\PaperForge",
+                "99_System/Zotero": f"{system_dir}/Zotero",
+                "99_System\\Zotero": f"{system_dir}\\Zotero",
+                "03_Resources/LiteratureControl": f"{resources_dir}/{control_dir}",
+                "03_Resources\\LiteratureControl": f"{resources_dir}\\{control_dir}",
+                "03_Resources/Literature": f"{resources_dir}/{literature_dir}",
+                "03_Resources\\Literature": f"{resources_dir}\\{literature_dir}",
+                ".opencode/skills": skill_dir_value or ".opencode/skills",
+                ".opencode\\skills": (skill_dir_value or ".opencode/skills").replace("/", "\\"),
+            }
+            for old, new in replacements.items():
+                text = text.replace(old, new)
+            return text
         
         # 1. 获取 agent 配置
         agent_config = getattr(self.app, 'agent_config', None)
@@ -892,8 +934,11 @@ class DeployStep(StepScreen):
         dirs = [
             pf_path / "exports",
             pf_path / "ocr",
+            pf_path / "config",
             pf_path / "worker/scripts",
-            vault / resources_dir / "LiteratureControl" / "library-records",
+            vault / resources_dir / literature_dir,
+            vault / resources_dir / control_dir / "library-records",
+            vault / base_dir,
             vault / skill_dir / "literature-qa/scripts",
             vault / skill_dir / "literature-qa/chart-reading",
         ]
@@ -920,6 +965,15 @@ class DeployStep(StepScreen):
         else:
             self.set_status(f"错误：找不到 ld_deep.py: {ld_src}", False)
             return False
+
+        # Copy subagent prompt
+        prompt_src = repo_root / "skills/literature-qa/prompt_deep_subagent.md"
+        prompt_dst = vault / skill_dir / "literature-qa/prompt_deep_subagent.md"
+        if prompt_src.exists():
+            shutil.copy2(prompt_src, prompt_dst)
+        else:
+            self.set_status(f"错误：找不到 prompt_deep_subagent.md: {prompt_src}", False)
+            return False
         
         # Copy chart-reading guides
         chart_src = repo_root / "skills/literature-qa/chart-reading"
@@ -927,11 +981,29 @@ class DeployStep(StepScreen):
         if chart_src.exists() and chart_src.is_dir():
             for f in chart_src.glob("*.md"):
                 shutil.copy2(f, chart_dst / f.name)
+
+        # Copy OpenCode command files when the target platform supports them.
+        if getattr(self.app, 'agent_key', '') == 'opencode':
+            command_src = repo_root / "command"
+            command_dst = vault / agent_config.get("command_dir", ".opencode/command")
+            if command_src.exists() and command_src.is_dir():
+                command_dst.mkdir(parents=True, exist_ok=True)
+                for f in command_src.glob("*.md"):
+                    text = apply_user_paths(f.read_text(encoding="utf-8"), skill_dir)
+                    (command_dst / f.name).write_text(text, encoding="utf-8")
+
+        # Copy user-facing docs. AGENTS.md is regenerated below with the chosen paths.
+        docs_src = repo_root / "docs"
+        docs_dst = vault / "docs"
+        if docs_src.exists() and docs_src.is_dir():
+            shutil.copytree(docs_src, docs_dst, dirs_exist_ok=True)
+            for doc in docs_dst.rglob("*.md"):
+                doc.write_text(apply_user_paths(doc.read_text(encoding="utf-8"), skill_dir), encoding="utf-8")
         
         # 5. 创建 .env（放到 PaperForge 目录下）
         from textual.widgets import Input
         api_key = self.query_one("#input-api-key", Input).value.strip()
-        api_url = self.query_one("#input-api-url", Input).value.strip() or "https://api.paddleocr.com/ocr"
+        api_url = self.query_one("#input-api-url", Input).value.strip() or "https://paddleocr.aistudio-app.com/api/v2/ocr/jobs"
         
         if not api_key:
             self.set_status("请填写 PaddleOCR API Key", False)
@@ -948,28 +1020,72 @@ PADDLEOCR_JOB_URL={api_url}
 
 # PaddleOCR 模型（通常不需要修改）
 PADDLEOCR_MODEL=PaddleOCR-VL-1.5
+
+# Zotero data directory selected during setup
+ZOTERO_DATA_DIR={getattr(self.app, 'zotero_data_dir', '')}
 """
         env_path.write_text(env_content, encoding="utf-8")
+
+        # Create a minimal domain mapping. The worker will keep this usable even
+        # before JSON exports exist, and will infer domains from export filenames.
+        domain_config = pf_path / "config" / "domain-collections.json"
+        if not domain_config.exists():
+            export_domains = [
+                {"domain": f.stem, "export_file": f.name, "allowed_collections": []}
+                for f in sorted((pf_path / "exports").glob("*.json"))
+            ]
+            domain_config.write_text(
+                json.dumps({"domains": export_domains}, indent=2, ensure_ascii=False),
+                encoding="utf-8",
+            )
         
         # 6. 创建 paperforge.json（包含用户自定义路径）
         pf_json = vault / "paperforge.json"
-        if not pf_json.exists():
-            import json
-            pf_json.write_text(json.dumps({
-                "version": "1.0.0",
-                "agent_platform": agent_config.get('name', 'OpenCode'),
-                "skill_dir": skill_dir,
+        existing_config = {}
+        if pf_json.exists():
+            try:
+                existing_config = json.loads(pf_json.read_text(encoding="utf-8"))
+            except Exception:
+                existing_config = {}
+        existing_config.update({
+            "version": existing_config.get("version", "1.2.0"),
+            "agent_platform": agent_config.get('name', 'OpenCode'),
+            "agent_key": getattr(self.app, 'agent_key', 'opencode'),
+            "skill_dir": skill_dir,
+            "command_dir": agent_config.get("command_dir", ""),
+            "system_dir": system_dir,
+            "resources_dir": resources_dir,
+            "literature_dir": literature_dir,
+            "control_dir": control_dir,
+            "base_dir": base_dir,
+            "paperforge_path": f"{system_dir}/PaperForge",
+            "zotero_data_dir": getattr(self.app, 'zotero_data_dir', ''),
+            "zotero_link": getattr(self.app, 'zotero_link', f"{system_dir}/Zotero"),
+            "vault_config": {
                 "system_dir": system_dir,
                 "resources_dir": resources_dir,
-                "paperforge_path": f"{system_dir}/PaperForge",
-            }, indent=2, ensure_ascii=False), encoding="utf-8")
+                "literature_dir": literature_dir,
+                "control_dir": control_dir,
+                "base_dir": base_dir,
+            },
+        })
+        pf_json.write_text(json.dumps(existing_config, indent=2, ensure_ascii=False), encoding="utf-8")
+
+        agents_src = repo_root / "AGENTS.md"
+        agents_dst = vault / "AGENTS.md"
+        if agents_src.exists():
+            agents_text = apply_user_paths(agents_src.read_text(encoding="utf-8"), skill_dir)
+            agents_dst.write_text(agents_text, encoding="utf-8")
         
         # 7. 验证文件完整性
         self.set_status("验证文件完整性...", None)
         checks = {
             "Worker 脚本": worker_dst.exists(),
             "精读脚本": ld_dst.exists(),
-            "目录结构": (vault / resources_dir / "LiteratureControl" / "library-records").exists(),
+            "精读提示词": prompt_dst.exists(),
+            "目录结构": (vault / resources_dir / control_dir / "library-records").exists(),
+            "Base 目录": (vault / base_dir).exists(),
+            "分类配置": domain_config.exists(),
             "导出目录": (pf_path / "exports").exists(),
             "OCR 目录": (pf_path / "ocr").exists(),
         }
@@ -1003,7 +1119,10 @@ class DoneStep(StepScreen):
 
     def compose(self) -> ComposeResult:
         yield from super().compose()
-        yield Markdown("""
+        vault_config = getattr(self.app, 'vault_config', {})
+        system_dir = vault_config.get('system_dir', '99_System')
+        worker_cmd = f"python {system_dir}/PaperForge/worker/scripts/literature_pipeline.py --vault ."
+        yield Markdown(f"""
 ## 安装完成！
 
 所有前置条件已满足，你现在可以开始使用 PaperForge Lite。
@@ -1012,12 +1131,12 @@ class DoneStep(StepScreen):
 
 **1. 同步 Zotero 文献**
 ```bash
-python 99_System/PaperForge/worker/scripts/literature_pipeline.py --vault . selection-sync
+{worker_cmd} selection-sync
 ```
 
 **2. 生成正式笔记**
 ```bash
-python 99_System/PaperForge/worker/scripts/literature_pipeline.py --vault . index-refresh
+{worker_cmd} index-refresh
 ```
 
 **3. 标记精读文献**
@@ -1027,7 +1146,7 @@ python 99_System/PaperForge/worker/scripts/literature_pipeline.py --vault . inde
 
 **4. 运行 OCR**
 ```bash
-python 99_System/PaperForge/worker/scripts/literature_pipeline.py --vault . ocr
+{worker_cmd} ocr
 ```
 
 **5. 执行精读**
@@ -1056,7 +1175,7 @@ python 99_System/PaperForge/worker/scripts/literature_pipeline.py --vault . ocr
 
 **Python 脚本命令（备用）：**
 ```bash
-python 99_System/PaperForge/worker/scripts/literature_pipeline.py --vault . <command>
+{worker_cmd} <command>
 ```
 | 命令 | 作用 |
 |------|------|

skills/literature-qa/prompt_deep_subagent.md

@@ -7,8 +7,8 @@
 ## 输入变量（由主 agent 填入）
 
 - `{{ZOTERO_KEY}}` — Zotero key，如 `Y5KQ4JQ7`
-- `{{VAULT}}` — Vault 根路径，如 `D:\L\Med\Research`
-- `{{SCRIPT}}` — `D:\L\Med\Research\.opencode\skills\literature-qa\scripts\ld_deep.py`
+- `{{VAULT}}` — Vault 根路径
+- `{{SCRIPT}}` — `<Vault>/<skill_dir>/literature-qa/scripts/ld_deep.py`
 
 ## 正确流程（必须按顺序执行）
 
@@ -36,8 +36,8 @@ python {{SCRIPT}} prepare {{ZOTERO_KEY}} --vault "{{VAULT}}" --format text
 - 这说明该论文已经精读过。如果用户要求重新精读，通知主 agent 确认是否覆盖。
 
 **prepare 成功后会自动生成以下文件**：
-- `99_System/PaperForge/ocr/{{ZOTERO_KEY}}/figure-map.json` — 图表清单
-- `99_System/PaperForge/ocr/{{ZOTERO_KEY}}/chart-type-map.json` — 图表类型与推荐指南
+- `<system_dir>/PaperForge/ocr/{{ZOTERO_KEY}}/figure-map.json` — 图表清单
+- `<system_dir>/PaperForge/ocr/{{ZOTERO_KEY}}/chart-type-map.json` — 图表类型与推荐指南
 
 **Agent 需要读取 chart-type-map.json**，为每张 figure 建立 `chart_types` 备忘列表。在 Pass 2 解析该 figure 时，根据其 chart_types 读取 `{{CHART_READING_DIR}}` 下对应的 chart-reading 指南，将关键审查问题整合进"图表质量审查"段落。
 
@@ -295,3 +295,4 @@ python {{SCRIPT}} validate-note "<note_path>" --fulltext "<fulltext_path>"
 # 列出待精读队列（信息用）
 python {{SCRIPT}} queue --vault "{{VAULT}}" --format table
 ```
+

skills/literature-qa/scripts/ld_deep.py

@@ -11,6 +11,41 @@ from pathlib import Path
 from typing import Iterable
 
 
+def _load_vault_config(vault: Path) -> dict:
+    """Load vault directory configuration from paperforge.json."""
+    defaults = {
+        "system_dir": "99_System",
+        "resources_dir": "03_Resources",
+        "literature_dir": "Literature",
+        "control_dir": "LiteratureControl",
+        "base_dir": "05_Bases",
+    }
+    config_path = vault / "paperforge.json"
+    if config_path.exists():
+        try:
+            data = json.loads(config_path.read_text(encoding="utf-8"))
+            nested = data.get("vault_config", {}) if isinstance(data.get("vault_config"), dict) else {}
+            return {**defaults, **nested, **{k: v for k, v in data.items() if k in defaults and v}}
+        except Exception:
+            pass
+    return defaults
+
+
+def _paperforge_paths(vault: Path) -> dict[str, Path]:
+    config = _load_vault_config(vault)
+    resources = vault / config["resources_dir"]
+    return {
+        "ocr": vault / config["system_dir"] / "PaperForge" / "ocr",
+        "records": resources / config["control_dir"] / "library-records",
+        "literature": resources / config["literature_dir"],
+    }
+
+
+def _get_ocr_root(vault: Path) -> Path:
+    """Get OCR root path dynamically from config."""
+    return _paperforge_paths(vault)["ocr"]
+
+
 STUDY_HEADER = "## 🔍 精读"
 FIGURE_SECTION_HEADER = "#### Figure-by-Figure 解析"
 TABLE_SECTION_HEADER = "#### Table-by-Table 解析"
@@ -542,8 +577,8 @@ def build_figure_map(fulltext: str, zotero_key: str = "") -> dict:
 
 
 def find_note_by_zotero_key(workspace_root: Path, zotero_key: str) -> Path | None:
-    """Resolve the formal literature note from 03_Resources/Literature."""
-    literature_root = workspace_root / "03_Resources" / "Literature"
+    """Resolve the formal literature note from the configured literature directory."""
+    literature_root = _paperforge_paths(workspace_root)["literature"]
     if not literature_root.exists():
         return None
 
@@ -953,9 +988,10 @@ def prepare_deep_reading(vault: Path, zotero_key: str, force: bool = False) -> d
         "chart_recommendations": [],
     }
 
-    records_root = vault / "03_Resources" / "LiteratureControl" / "library-records"
-    literature_root = vault / "03_Resources" / "Literature"
-    ocr_root = vault / "99_System" / "LiteraturePipeline" / "ocr"
+    paths = _paperforge_paths(vault)
+    records_root = paths["records"]
+    literature_root = paths["literature"]
+    ocr_root = paths["ocr"]
 
     # 1. Find library-record
     record_path: Path | None = None
@@ -1116,8 +1152,9 @@ def scan_deep_reading_queue(vault: Path) -> list[dict]:
     Returns a list of dicts with keys:
       - zotero_key, title, domain, analyze, deep_reading_status, ocr_status
     """
-    records_root = vault / "03_Resources" / "LiteratureControl" / "library-records"
-    ocr_root = vault / "99_System" / "LiteraturePipeline" / "ocr"
+    paths = _paperforge_paths(vault)
+    records_root = paths["records"]
+    ocr_root = paths["ocr"]
     queue: list[dict] = []
     if not records_root.exists():
         return queue

update.py

@@ -47,16 +47,6 @@ if sys.platform == "win32":
     sys.stdout = io.TextIOWrapper(sys.stdout.buffer, encoding="utf-8")
     sys.stderr = io.TextIOWrapper(sys.stderr.buffer, encoding="utf-8")
 
-# 用户数据保护清单（绝不动这些路径）
-PROTECTED_PATHS = {
-    "03_Resources", "05_Bases",
-    "99_System/PaperForge/ocr",
-    "99_System/PaperForge/exports",
-    "99_System/PaperForge/indexes",
-    "99_System/PaperForge/candidates",
-    ".env", "AGENTS.md",
-}
-
 # 可更新路径（代码文件）
 UPDATEABLE_PATHS = ["skills", "pipeline", "command", "scripts"]
 
@@ -83,6 +73,34 @@ def load_json(path: Path) -> dict:
     return json.loads(path.read_text(encoding="utf-8")) if path.exists() else {}
 
 
+def load_vault_config(vault: Path) -> dict:
+    defaults = {
+        "system_dir": "99_System",
+        "resources_dir": "03_Resources",
+        "literature_dir": "Literature",
+        "control_dir": "LiteratureControl",
+        "base_dir": "05_Bases",
+    }
+    data = load_json(vault / "paperforge.json")
+    nested = data.get("vault_config", {}) if isinstance(data.get("vault_config"), dict) else {}
+    return {**defaults, **nested, **{k: v for k, v in data.items() if k in defaults and v}}
+
+
+def protected_paths(vault: Path) -> set[str]:
+    cfg = load_vault_config(vault)
+    pf = f"{cfg['system_dir']}/PaperForge"
+    return {
+        cfg["resources_dir"],
+        cfg["base_dir"],
+        f"{pf}/ocr",
+        f"{pf}/exports",
+        f"{pf}/indexes",
+        f"{pf}/candidates",
+        ".env",
+        "AGENTS.md",
+    }
+
+
 def sha256(path: Path) -> str:
     return hashlib.sha256(path.read_bytes()).hexdigest() if path.exists() else ""
 
@@ -137,6 +155,7 @@ def newer(a: str, b: str) -> bool:
 def scan_updates(vault: Path, source: Path) -> list[tuple[Path, Path, str]]:
     """扫描需要更新的文件，返回 (src, dst, action) 列表"""
     updates = []
+    protected = protected_paths(vault)
     for name in UPDATEABLE_PATHS:
         src_dir = source / name
         if not src_dir.exists():
@@ -147,7 +166,7 @@ def scan_updates(vault: Path, source: Path) -> list[tuple[Path, Path, str]]:
             rel = src.relative_to(source)
             dst = vault / rel
             rel_str = str(rel).replace("\\", "/")
-            if any(rel_str.startswith(p) for p in PROTECTED_PATHS):
+            if any(rel_str.startswith(p) for p in protected):
                 continue
             if dst.exists():
                 if sha256(src) != sha256(dst):