diff --git a/.gitignore b/.gitignore
index a675e4d2..c44a0519 100644
--- 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/
 
diff --git a/AGENTS.md b/AGENTS.md
index f26a4db1..ce71dfb9 100644
--- 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）
 
 ---
 
diff --git a/command/ld-deep.md b/command/ld-deep.md
index ddc97421..c646b929 100644
--- 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
diff --git a/command/lp-index-refresh.md b/command/lp-index-refresh.md
index 447e1b1b..3855fcfa 100644
--- 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
diff --git a/command/lp-ocr.md b/command/lp-ocr.md
index 12420a3a..11817159 100644
--- 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
 ```
\ No newline at end of file
diff --git a/command/lp-selection-sync.md b/command/lp-selection-sync.md
index 1d37cbb9..8cbdf460 100644
--- 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
 ```
\ No newline at end of file
diff --git a/command/lp-status.md b/command/lp-status.md
index cfb60588..2aef4bf2 100644
--- 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')"
 ```
\ No newline at end of file
diff --git a/docs/INSTALLATION.md b/docs/INSTALLATION.md
index 85903b02..679354cc 100644
--- 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
    ```
 
 ---
diff --git a/docs/setup-guide.md b/docs/setup-guide.md
index 3516a212..c214e7ec 100644
--- 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  ...
 ```
 
diff --git a/paperforge.json b/paperforge.json
index a012c56c..f02335e7 100644
--- 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"
   ],
diff --git a/pipeline/worker/scripts/literature_pipeline.py b/pipeline/worker/scripts/literature_pipeline.py
index db54af4b..8d00d774 100644
--- 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"]
diff --git a/scripts/setup.py b/scripts/setup.py
index 19f6228e..c1c1dd47 100644
--- 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）
diff --git a/setup_wizard.py b/setup_wizard.py
index b0621e5a..e53dde7d 100644
--- 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
 
 
diff --git a/skills/literature-qa/prompt_deep_subagent.md b/skills/literature-qa/prompt_deep_subagent.md
index ff3b7b05..4cb321c0 100644
--- 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。
 
diff --git a/update.py b/update.py
index fb71379c..b7d084a3 100644
--- 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",
 }