rename: LiteraturePipeline -> PaperForge in all paths and references

2026-07-22 06:50:53 +00:00 · 2026-04-22 22:10:16 +08:00 · 2026-04-22 22:10:16 +08:00 · c607dd0441
commit c607dd0441
parent 19292e1eee
15 changed files with 129 additions and 81 deletions
--- a/.gitignore
+++ b/.gitignore
@ -21,7 +21,7 @@ config.json

 # Data (user-specific)
 99_System/Zotero/
-99_System/LiteraturePipeline/ocr/
+99_System/PaperForge/ocr/
 00_Inbox/
 03_Resources/

--- a/AGENTS.md
+++ b/AGENTS.md
@ -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/LiteraturePipeline/exports/library.json`
+4. 导出路径设置为：`{你的Vault路径}/99_System/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/LiteraturePipeline/exports/library.json
+99_System/PaperForge/exports/library.json
    ↓ 运行 selection-sync
 03_Resources/LiteratureControl/library-records/<domain>/<key>.md
    ↓ 运行 index-refresh
 03_Resources/Literature/<domain>/<key> - <Title>.md（正式笔记）
    ↓ 用户在 library-record 中设置 do_ocr: true
-运行 ocr → 99_System/LiteraturePipeline/ocr/<key>/
+运行 ocr → 99_System/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
@ -114,8 +114,8 @@ Zotero 添加文献
 |------|------|------------|
 | `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/LiteraturePipeline/exports/` | Better BibTeX JSON 导出 | Zotero 自动导出 |
-| `99_System/LiteraturePipeline/ocr/` | OCR 全文 + 图表切割 | ocr worker 生成 |
+| `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 |

 ---
@ -128,7 +128,7 @@ Zotero 添加文献
 - **输出**：`03_Resources/LiteratureControl/library-records/<domain>/<key>.md`
 - **示例**：
  ```bash
-  python 99_System/LiteraturePipeline/worker/scripts/literature_pipeline.py \
+  python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
    --vault "{vault路径}" selection-sync
  ```

@ -141,7 +141,7 @@ Zotero 添加文献
 ### 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/LiteraturePipeline/ocr/<key>/` 目录
+- **输出**：`99_System/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`）
@ -201,7 +201,7 @@ 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/LiteraturePipeline/ocr/..."
+fulltext_md_path: "99_System/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
@ -249,7 +249,7 @@ pdf_link: "99_System/Zotero/..."

 ```bash
 # 在 Vault 根目录执行
-python 99_System/LiteraturePipeline/worker/scripts/literature_pipeline.py \
+python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
  --vault "你的Vault路径" selection-sync
 ```

@ -263,7 +263,7 @@ python 99_System/LiteraturePipeline/worker/scripts/literature_pipeline.py \
 ### Step 3: 运行 index-refresh

 ```bash
-python 99_System/LiteraturePipeline/worker/scripts/literature_pipeline.py \
+python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
  --vault "你的Vault路径" index-refresh
 ```

@ -285,7 +285,7 @@ python 99_System/LiteraturePipeline/worker/scripts/literature_pipeline.py \
 ### Step 5: 运行 OCR

 ```bash
-python 99_System/LiteraturePipeline/worker/scripts/literature_pipeline.py \
+python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
  --vault "你的Vault路径" ocr
 ```

@ -294,7 +294,7 @@ python 99_System/LiteraturePipeline/worker/scripts/literature_pipeline.py \
 ### Step 6: 检查 OCR 状态

 ```bash
-python 99_System/LiteraturePipeline/worker/scripts/literature_pipeline.py \
+python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
  --vault "你的Vault路径" deep-reading
 ```

@ -326,23 +326,23 @@ Agent 会自动：

 ```bash
 # 检测 Zotero 新条目
-python 99_System/LiteraturePipeline/worker/scripts/literature_pipeline.py \
+python 99_System/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/LiteraturePipeline/worker/scripts/literature_pipeline.py \
+python 99_System/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/LiteraturePipeline/worker/scripts/literature_pipeline.py \
+python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
  --vault "你的Vault路径" ocr

 # 查看精读队列
-python 99_System/LiteraturePipeline/worker/scripts/literature_pipeline.py \
+python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
  --vault "你的Vault路径" deep-reading

 # 查看整体状态
-python 99_System/LiteraturePipeline/worker/scripts/literature_pipeline.py \
+python 99_System/PaperForge/worker/scripts/literature_pipeline.py \
  --vault "你的Vault路径" status
 ```

@ -364,7 +364,7 @@ python 99_System/LiteraturePipeline/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/LiteraturePipeline/ocr/<key>/meta.json` 中的错误信息
+- 查看 `99_System/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`
@ -389,13 +389,13 @@ 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/LiteraturePipeline/worker/scripts/
+cp -r 新下载的scripts/* 99_System/PaperForge/worker/scripts/
 ```

 ### 备份注意事项
- `03_Resources/` 和 `99_System/LiteraturePipeline/ocr/` 包含你的数据，需备份
+- `03_Resources/` 和 `99_System/PaperForge/ocr/` 包含你的数据，需备份
 - `.env` 包含 API Key，不要提交到 git
- `99_System/LiteraturePipeline/exports/` 可重新生成（由 Zotero 自动导出）
+- `99_System/PaperForge/exports/` 可重新生成（由 Zotero 自动导出）

 ---

--- a/command/ld-deep.md
+++ b/command/ld-deep.md
@ -8,8 +8,8 @@
 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/LiteraturePipeline/ocr/<KEY>/fulltext.md`
-   - `99_System/LiteraturePipeline/ocr/<KEY>/meta.json`
+   - `99_System/PaperForge/ocr/<KEY>/fulltext.md`
+   - `99_System/PaperForge/ocr/<KEY>/meta.json`
   - `03_Resources/Literature/.../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
--- a/command/lp-index-refresh.md
+++ b/command/lp-index-refresh.md
@ -5,7 +5,7 @@
 ## Commands

 ```bash
-python 99_System/LiteraturePipeline/worker/scripts/literature_pipeline.py --vault D:\L\Med\Research index-refresh
+python 99_System/PaperForge/worker/scripts/literature_pipeline.py --vault D:\L\Med\Research index-refresh
 ```

 ## 输出示例
--- a/command/lp-ocr.md
+++ b/command/lp-ocr.md
@ -5,5 +5,5 @@
 ## Commands

 ```bash
-python 99_System/LiteraturePipeline/worker/scripts/literature_pipeline.py --vault D:\L\Med\Research ocr
+python 99_System/PaperForge/worker/scripts/literature_pipeline.py --vault D:\L\Med\Research ocr
 ```
--- a/command/lp-selection-sync.md
+++ b/command/lp-selection-sync.md
@ -5,5 +5,5 @@
 ## Commands

 ```bash
-python 99_System/LiteraturePipeline/worker/scripts/literature_pipeline.py --vault D:\L\Med\Research selection-sync
+python 99_System/PaperForge/worker/scripts/literature_pipeline.py --vault D:\L\Med\Research selection-sync
 ```
--- a/command/lp-status.md
+++ b/command/lp-status.md
@ -5,7 +5,7 @@
 ## 检查 exports 记录数

 ```bash
-python -c "import json; from pathlib import Path; data = json.loads(Path('99_System/LiteraturePipeline/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 -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')"
 ```

 ## 检查 library-records 总数
@ -17,11 +17,11 @@ python -c "from pathlib import Path; count = sum(1 for _ in Path('03_Resources/L
 ## 检查 OCR 完成数

 ```bash
-python -c "from pathlib import Path; done = sum(1 for p in Path('99_System/LiteraturePipeline/ocr').glob('*/meta.json') if 'done' in Path(p).read_text('utf-8')); print(f'OCR done: {done}')"
+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/LiteraturePipeline/indexes/formal-library.json', encoding='utf-8')); print(f'Index: {len(data)} records')"
+python -c "import json; data = json.load(open('99_System/PaperForge/indexes/formal-library.json', encoding='utf-8')); print(f'Index: {len(data)} records')"
 ```
--- a/docs/INSTALLATION.md
+++ b/docs/INSTALLATION.md
@ -64,8 +64,8 @@ poetry add requests pymupdf pillow pytest
 Create the following directories in the Obsidian vault:

 ```bash
-mkdir -p "{vault_path}/99_System/LiteraturePipeline/ocr"
-mkdir -p "{vault_path}/99_System/LiteraturePipeline/worker/scripts"
+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/Literature"
 mkdir -p "{vault_path}/00_Inbox"
@ -113,7 +113,7 @@ Copy the following files from the repository to your vault:

 ```bash
 # Copy scripts
-cp -r scripts/* "{vault_path}/99_System/LiteraturePipeline/worker/scripts/"
+cp -r scripts/* "{vault_path}/99_System/PaperForge/worker/scripts/"

 # Copy templates
 cp -r templates/* "{vault_path}/99_System/Template/"
@ -130,7 +130,7 @@ Run validation:

 ```bash
 cd "{vault_path}"
-python 99_System/LiteraturePipeline/worker/scripts/validate_setup.py
+python 99_System/PaperForge/worker/scripts/validate_setup.py
 ```

 This checks:
@ -170,7 +170,7 @@ Edit `{vault_path}/AGENTS.md`:

 3. **Verify**:
   ```bash
-   python 99_System/LiteraturePipeline/worker/scripts/validate_setup.py
+   python 99_System/PaperForge/worker/scripts/validate_setup.py
   ```

 ---
--- a/docs/setup-guide.md
+++ b/docs/setup-guide.md
@ -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/LiteraturePipeline/exports/
+            └─ 保存位置: {你的Vault}/99_System/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/LiteraturePipeline/exports/
+   {你的Vault根目录}/99_System/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/LiteraturePipeline/exports/
+ls 99_System/PaperForge/exports/
 # 应该看到: 骨科.json  运动医学.json  ...
 ```

--- a/paperforge.json
+++ b/paperforge.json
@ -11,10 +11,10 @@
  "protected_paths": [
    "03_Resources/",
    "05_Bases/",
-    "99_System/LiteraturePipeline/ocr/",
-    "99_System/LiteraturePipeline/exports/",
-    "99_System/LiteraturePipeline/indexes/",
-    "99_System/LiteraturePipeline/candidates/",
+    "99_System/PaperForge/ocr/",
+    "99_System/PaperForge/exports/",
+    "99_System/PaperForge/indexes/",
+    "99_System/PaperForge/candidates/",
    ".env",
    "AGENTS.md"
  ],
--- a/pipeline/worker/scripts/literature_pipeline.py
+++ b/pipeline/worker/scripts/literature_pipeline.py
@ -1175,7 +1175,7 @@ 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/LiteraturePipeline/ocr/{key}/images')
+    meta.setdefault('assets_path', f'99_System/PaperForge/ocr/{key}/images')
    meta.setdefault('fulltext_md_path', '')
    meta.setdefault('error', '')
    return meta
@ -2385,10 +2385,10 @@ GITHUB_ZIP = f"https://github.com/{GITHUB_REPO}/archive/refs/heads/master.zip"

 PROTECTED_PATHS = {
    "03_Resources", "05_Bases",
-    "99_System/LiteraturePipeline/ocr",
-    "99_System/LiteraturePipeline/exports",
-    "99_System/LiteraturePipeline/indexes",
-    "99_System/LiteraturePipeline/candidates",
+    "99_System/PaperForge/ocr",
+    "99_System/PaperForge/exports",
+    "99_System/PaperForge/indexes",
+    "99_System/PaperForge/candidates",
    ".env", "AGENTS.md",
 }
 UPDATEABLE_PATHS = ["skills", "pipeline", "templates", "command", "scripts"]
--- a/scripts/setup.py
+++ b/scripts/setup.py
@ -115,7 +115,7 @@ def configure_vault_paths(vault_path: Path) -> dict:
    }
    
    # Build derived paths
-    paths["pipeline_path"] = f"{paths['system_dir']}/LiteraturePipeline"
+    paths["pipeline_path"] = f"{paths['system_dir']}/PaperForge"
    paths["template_path"] = f"{paths['system_dir']}/Template"
    paths["literature_path"] = f"{paths['resources_dir']}/{paths['literature_dir']}"
    
@ -401,7 +401,7 @@ Zotero 添加文献
 │               └── HIJKLMN.md
 │
 ├── {paths['system_dir']}/
-│   ├── LiteraturePipeline/
+│   ├── 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）
--- a/setup_wizard.py
+++ b/setup_wizard.py
@ -72,6 +72,7 @@ class EnvChecker:
    def __init__(self, vault: Path):
        self.vault = vault
        self.manual_zotero_path: Optional[Path] = None
+        self.system_dir: str = "99_System"  # 可由用户自定义
        self.results: dict[str, CheckResult] = {
            "python": CheckResult("Python 版本"),
            "vault": CheckResult("Vault 结构"),
@ -80,6 +81,10 @@ class EnvChecker:
            "json": CheckResult("JSON 导出"),
        }

+    def get_exports_dir(self) -> Path:
+        """Get exports directory based on user config."""
+        return self.vault / self.system_dir / "PaperForge" / "exports"
+
    def check_python(self) -> CheckResult:
        r = self.results["python"]
        v = sys.version_info
@ -121,10 +126,8 @@ class EnvChecker:
    def check_vault(self) -> CheckResult:
        r = self.results["vault"]
        required = [
-            "03_Resources/LiteratureControl/library-records",
-            "99_System/LiteraturePipeline/exports",
-            "99_System/LiteraturePipeline/ocr",
-            "99_System/Template",
+            f"{self.system_dir}/PaperForge/exports",
+            f"{self.system_dir}/PaperForge/ocr",
        ]
        missing = [rel for rel in required if not (self.vault / rel).exists()]
        if not missing:
@ -135,6 +138,12 @@ class EnvChecker:
            r.detail = f"缺少: {', '.join(missing)}"
            r.action_required = True
        return r
+            r.detail = "所有必要目录已就绪"
+        else:
+            r.passed = False
+            r.detail = f"缺少: {', '.join(missing)}"
+            r.action_required = True
+        return r

    def _find_zotero(self, manual_path: Optional[Path] = None) -> Optional[Path]:
        # 如果提供了手动路径，优先使用
@ -283,7 +292,7 @@ class EnvChecker:

    def check_json(self) -> CheckResult:
        r = self.results["json"]
-        exports_dir = self.vault / "99_System" / "LiteraturePipeline" / "exports"
+        exports_dir = self.get_exports_dir()
        if not exports_dir.exists():
            r.passed = False
            r.detail = f"导出目录不存在: {exports_dir}"
@ -489,9 +498,8 @@ PaperForge 的目录结构可以自定义。你可以保留默认名称，也可
 {vault_path.name}/
 ├── 03_Resources/          ← 文献笔记和资源
 │   └── LiteratureControl/   ← 状态跟踪
-├── 99_System/             ← 系统文件
-│   ├── LiteraturePipeline/  ← 导出和 OCR
-│   └── Template/            ← 模板
+└── 99_System/             ← 系统文件
+    └── PaperForge/          ← 导出和 OCR
 ```

 修改下方名称（留空使用默认值）：
@ -504,7 +512,7 @@ PaperForge 的目录结构可以自定义。你可以保留默认名称，也可
        yield Static("文献子文件夹名称:", classes="step-title")
        yield Input(value="Literature", id="input-literature-dir")
        yield Horizontal(
-            Button("🔍 检测并创建目录", id="btn-setup-vault", variant="primary"),
+            Button("✓ 确认并创建目录", id="btn-setup-vault", variant="primary"),
            id="btn-row",
        )

@ -520,18 +528,16 @@ PaperForge 的目录结构可以自定义。你可以保留默认名称，也可
                "system_dir": system_dir,
                "resources_dir": resources_dir,
                "literature_dir": literature_dir,
-                "pipeline_path": f"{system_dir}/LiteraturePipeline",
-                "template_path": f"{system_dir}/Template",
+                "paperforge_path": f"{system_dir}/PaperForge",
                "literature_path": f"{resources_dir}/{literature_dir}",
            }

-            # 创建目录
+            # 创建目录（使用 PaperForge 作为统一子目录）
            vault = self.checker.vault
            dirs_to_create = [
                vault / resources_dir / "LiteratureControl" / "library-records",
-                vault / system_dir / "LiteraturePipeline" / "exports",
-                vault / system_dir / "LiteraturePipeline" / "ocr",
-                vault / system_dir / "Template",
+                vault / system_dir / "PaperForge" / "exports",
+                vault / system_dir / "PaperForge" / "ocr",
            ]

            created = []
@ -539,7 +545,10 @@ PaperForge 的目录结构可以自定义。你可以保留默认名称，也可
                d.mkdir(parents=True, exist_ok=True)
                created.append(str(d.relative_to(vault)))

-            self.set_status(f"已创建 {len(created)} 个目录", True)
+            # 同步更新 checker 的 system_dir
+            self.checker.system_dir = system_dir
+
+            self.set_status(f"已创建 {len(created)} 个目录: {', '.join(created)}", True)
            self.app.post_message(StepPassed(self.step_idx))


@ -660,21 +669,23 @@ class BBTStep(StepScreen):


 class JsonStep(StepScreen):
-    """Step 6: JSON Export"""
+    """Step 5: JSON 导出配置"""

    def compose(self) -> ComposeResult:
        yield from super().compose()
-        exports_dir = self.checker.vault / "99_System" / "LiteraturePipeline" / "exports"
+        vault = self.checker.vault
+        system_dir = getattr(self.app, 'vault_config', {}).get('system_dir', '99_System')
+        exports_dir = vault / system_dir / "PaperForge" / "exports"
        yield Markdown(f"""
 **Better BibTeX 自动导出**是 PaperForge 的数据来源。

 **配置步骤：**
 1. Zotero → 文件 → 导出库...
 2. 格式选择 **Better BibLaTeX**
-3. 保存到：`{exports_dir}/library.json`
+3. 保存到：`{exports_dir}`
 4. 勾选 **Keep updated**（自动保持更新）

-**📁 子分类与 Base 管理**
+📁 **子分类与 Base 管理**

 你可以根据 Zotero 收藏夹结构，灵活决定如何导出：

@ -701,7 +712,6 @@ Zotero 收藏夹结构
        """)
        yield Horizontal(
            Button("🔍 自动检测", id="btn-check-json", variant="primary"),
-            Button("📷 查看配置截图", id="btn-img-json", variant="default"),
            id="btn-row",
        )

@ -711,8 +721,6 @@ Zotero 收藏夹结构
            self.set_status(result.detail, result.passed)
            if result.passed:
                self.app.post_message(StepPassed(self.step_idx))
-        elif event.button.id == "btn-img-json":
-            self.app.open_screenshot("json-export.png")


 class DeployStep(StepScreen):
@ -749,6 +757,9 @@ class DeployStep(StepScreen):
    def _deploy(self) -> bool:
        """Deploy scripts and create config files."""
        vault = self.checker.vault
+        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')
        
        # 1. 获取 agent 配置
        agent_config = getattr(self.app, 'agent_config', None)
@ -758,12 +769,15 @@ class DeployStep(StepScreen):
        
        skill_dir = agent_config.get('skill_dir', '.opencode/skills')
        
-        # 2. 创建目录
+        # 2. 创建目录（使用用户自定义路径）
+        pf_path = vault / system_dir / "PaperForge"
        dirs = [
+            pf_path / "exports",
+            pf_path / "ocr",
+            vault / resources_dir / "LiteratureControl" / "library-records",
            vault / "pipeline/worker/scripts",
            vault / skill_dir / "literature-qa/scripts",
            vault / skill_dir / "literature-qa/chart-reading",
-            vault / "99_System/Template",
        ]
        for d in dirs:
            d.mkdir(parents=True, exist_ok=True)
@ -802,7 +816,7 @@ PADDLEOCR_API_KEY=your_api_key_here
 PADDLEOCR_API_URL=https://api.paddleocr.com/ocr
 """, encoding="utf-8")
        
-        # 5. 创建 paperforge.json
+        # 5. 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
@ -810,8 +824,42 @@ PADDLEOCR_API_URL=https://api.paddleocr.com/ocr
                "version": "1.0.0",
                "agent_platform": agent_config.get('name', 'OpenCode'),
                "skill_dir": skill_dir,
+                "system_dir": system_dir,
+                "resources_dir": resources_dir,
+                "paperforge_path": f"{system_dir}/PaperForge",
            }, indent=2, ensure_ascii=False), encoding="utf-8")
        
+        # 6. 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(),
+            "导出目录": (pf_path / "exports").exists(),
+            "OCR 目录": (pf_path / "ocr").exists(),
+        }
+        
+        missing = [k for k, v in checks.items() if not v]
+        if missing:
+            self.set_status(f"验证失败: {', '.join(missing)}", False)
+            return False
+        
+        self.set_status("文件验证通过，初始化系统...", True)
+        
+        # 7. 运行初始化命令（模拟测试）
+        try:
+            # 测试 selection-sync（会报错因为没 JSON，但测试脚本能否运行）
+            result = subprocess.run(
+                [sys.executable, str(worker_dst), "--vault", str(vault), "status"],
+                capture_output=True, text=True, timeout=10,
+            )
+            if result.returncode == 0:
+                self.set_status("工作流脚本运行正常", True)
+            else:
+                self.set_status(f"脚本测试警告: {result.stderr[:100]}", None)
+        except Exception as e:
+            self.set_status(f"脚本测试跳过: {e}", None)
+        
        return True


--- a/skills/literature-qa/prompt_deep_subagent.md
+++ b/skills/literature-qa/prompt_deep_subagent.md
@ -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/LiteraturePipeline/ocr/{{ZOTERO_KEY}}/figure-map.json` — 图表清单
- `99_System/LiteraturePipeline/ocr/{{ZOTERO_KEY}}/chart-type-map.json` — 图表类型与推荐指南
+- `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

 **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。

--- a/update.py
+++ b/update.py
@ -50,10 +50,10 @@ if sys.platform == "win32":
 # 用户数据保护清单（绝不动这些路径）
 PROTECTED_PATHS = {
    "03_Resources", "05_Bases",
-    "99_System/LiteraturePipeline/ocr",
-    "99_System/LiteraturePipeline/exports",
-    "99_System/LiteraturePipeline/indexes",
-    "99_System/LiteraturePipeline/candidates",
+    "99_System/PaperForge/ocr",
+    "99_System/PaperForge/exports",
+    "99_System/PaperForge/indexes",
+    "99_System/PaperForge/candidates",
    ".env", "AGENTS.md",
 }