fix(skill): split vault-browse from paper-search, add browsing flow to vault-knowledge

paperforge/setup/runtime.py

@@ -38,6 +38,8 @@ class RuntimeInstaller:
                 [sys.executable, "-m", "pip", "install", package_spec],
                 capture_output=True,
                 text=True,
+                encoding="utf-8",
+                errors="replace",
                 timeout=120,
             )
             return (result.returncode == 0, result.stdout, result.stderr)
@@ -96,6 +98,8 @@ class RuntimeInstaller:
                 ],
                 capture_output=True,
                 text=True,
+                encoding="utf-8",
+                errors="replace",
                 timeout=10,
             )
             return result.returncode == 0 and bool(result.stdout.strip())

paperforge/setup/vault.py

@@ -80,6 +80,8 @@ class VaultInitializer:
                     ["cmd", "/c", "mklink", "/J", str(zotero_link), zotero_path],
                     capture_output=True,
                     text=True,
+                    encoding="utf-8",
+                    errors="replace",
                     timeout=30,
                 )
                 if result.returncode != 0:

paperforge/setup_wizard.py

@@ -118,7 +118,7 @@ class EnvChecker:
     def install_dependencies(self) -> bool:
         deps = ["requests", "pymupdf", "pillow"]
         try:
-            subprocess.run([sys.executable, "-m", "pip", "install"] + deps, check=True, capture_output=True)
+            subprocess.run([sys.executable, "-m", "pip", "install"] + deps, check=True, capture_output=True, encoding="utf-8", errors="replace")
             return True
         except subprocess.CalledProcessError:
             return False
@@ -178,7 +178,7 @@ class EnvChecker:
                     return p
             # 4. 通过 where 命令检测
             try:
-                result = subprocess.run(["where", "zotero"], capture_output=True, text=True, timeout=5)
+                result = subprocess.run(["where", "zotero"], capture_output=True, text=True, encoding="utf-8", errors="replace", timeout=5)
                 if result.returncode == 0:
                     for line in result.stdout.strip().split("\n"):
                         p = Path(line.strip())
@@ -196,7 +196,7 @@ class EnvChecker:
                     return p
             # 通过 which 检测
             try:
-                result = subprocess.run(["which", "zotero"], capture_output=True, text=True, timeout=5)
+                result = subprocess.run(["which", "zotero"], capture_output=True, text=True, encoding="utf-8", errors="replace", timeout=5)
                 if result.returncode == 0:
                     return Path(result.stdout.strip())
             except Exception:
@@ -213,7 +213,7 @@ class EnvChecker:
                 if p.exists():
                     return p
             try:
-                result = subprocess.run(["which", "zotero"], capture_output=True, text=True, timeout=5)
+                result = subprocess.run(["which", "zotero"], capture_output=True, text=True, encoding="utf-8", errors="replace", timeout=5)
                 if result.returncode == 0:
                     return Path(result.stdout.strip())
             except Exception:
@@ -527,6 +527,8 @@ def headless_setup(
                         ["cmd", "/c", "mklink", "/J", str(zotero_link_path), str(zotero_data)],
                         capture_output=True,
                         text=True,
+                        encoding="utf-8",
+                        errors="replace",
                         timeout=30,
                     )
                     if result.returncode != 0:
@@ -767,6 +769,8 @@ def headless_setup(
                 [sys.executable, "-m", "pip", "install", "--upgrade"] + install_target,
                 capture_output=True,
                 text=True,
+                encoding="utf-8",
+                errors="replace",
                 timeout=120,
             )
             if result.returncode != 0:
@@ -775,6 +779,8 @@ def headless_setup(
                     [sys.executable, "-m", "pip", "install", "--upgrade"] + git_target,
                     capture_output=True,
                     text=True,
+                    encoding="utf-8",
+                    errors="replace",
                     timeout=120,
                 )
         if result.returncode == 0:
@@ -782,6 +788,8 @@ def headless_setup(
                 [sys.executable, "-c", "import paperforge; print(getattr(paperforge, '__version__', '?'))"],
                 capture_output=True,
                 text=True,
+                encoding="utf-8",
+                errors="replace",
                 timeout=15,
             )
             new_ver = _new.stdout.strip() or "?"

paperforge/skills/literature-qa/SKILL.md

@@ -21,7 +21,8 @@ Agent 读到本文件后，首先根据用户意图路由到对应的 reference
 
 | 用户意图 | 典型输入 | 加载文件 |
 |---------|---------|---------|
-| 文献检索 | "找一下骨科...文献", "查一下 TGF-beta", "库里有没有支架材料的", "搜一下 Smith 的文章", "collection 里有没有", "看一下库里内容", "看一下文献库", "库里有什么", "浏览文献" | [references/paper-search.md](references/paper-search.md) |
+| 查看 Vault 概况 | "看一下库里内容", "看一下文献库", "库里有什么", "浏览文献" | [references/vault-knowledge.md](references/vault-knowledge.md) |
+| 文献检索 | "找一下骨科...文献", "查一下 TGF-beta", "库里有没有支架材料的", "搜一下 Smith 的文章", "collection 里有没有" | [references/paper-search.md](references/paper-search.md) |
 | 三阶段精读（指定论文） | `/pf-deep <query>`, `pf-deep <query>`, "精读 XXX", "深度阅读 XXX", "带我读", "组会讲这篇", "读一下这篇" | [references/deep-reading.md](references/deep-reading.md) |
 | 三阶段精读（查看队列） | `/pf-deep`（无参数）, "精读队列", "有哪些该读了" | [references/deep-reading.md](references/deep-reading.md) |
 | 论文问答 | `/pf-paper <query>`, `pf-paper <query>`, "做这篇的问答", "帮我看看 XXX", "这篇文章讲了什么", "查一下" | [references/paper-qa.md](references/paper-qa.md) |

paperforge/skills/literature-qa/references/paper-search.md

@@ -11,8 +11,6 @@
 - "库里有没有讲支架材料的"
 - "这个 collection 有哪些文献"
 - "搜一下 Smith 2024 的文章"
-- "看一下库里内容" / "看一下文献库"
-- "库里有什么" / "浏览文献"
 
 ## 流程
 
@@ -67,6 +65,16 @@ Agent 直接读 `index_path`，在 JSON 中筛选：
 - `这篇讲了什么` → 进入 [paper-qa.md](paper-qa.md) 流程
 - 不需要继续 → 结束
 
+### Step 6: 写作辅助场景
+
+如果用户原始意图包含**写作/优化/参考文献/综述/引用**等，搜索结果不是终点：
+
+1. 提示用户圈选最相关的 3-5 篇
+2. 对每篇进入 [deep-reading.md](deep-reading.md) 或至少通读 formal note + fulltext 关键段落
+3. 读完所有选定论文后，Agent 整合知识辅助写作
+
+> 示例："我从库里 X 篇文献中提取了以下关键发现……要不要基于这些帮你写 XX 部分？"
+
 ## 注意事项
 
 - 如果是大型 library（>500 篇），优先用 paper_resolver 而不是全量读 JSON

paperforge/skills/literature-qa/references/vault-knowledge.md

@@ -2,6 +2,22 @@
 
 本文件是 Agent 理解 PaperForge Vault 的共享参考。精读、问答、检索等所有工作流都先从这里获取基础概念。
 
+## 浏览场景
+
+用户说"看一下库里内容"、"看一下文献库"、"库里有什么"、"浏览文献"时，Agent 展示 Vault 概况：
+
+1. 跑 `paths` 获取 `literature_dir` 和 `index_path`
+2. 列出 `literature_dir` 下所有 domain（领域文件夹名）
+3. 读 formal-library.json，统计每个 domain：论文总数、OCR 完成数、无 PDF 数
+4. 输出概览：
+
+```
+Vault: D:\...\Vault
+Domains: 骨科 (550 papers, 520 OCR done), 运动医学 (263 papers, 129 OCR done)
+```
+
+如果用户继续问具体内容，Agent 加载 [paper-search.md](paper-search.md) 搜索。
+
 ---
 
 ## 1. 获取路径

paperforge/worker/status.py

@@ -278,8 +278,7 @@ def _resolve_plugin_interpreter(vault: Path, plugin_data: dict) -> tuple[str, st
     for path, extra in system_candidates:
         try:
             cmd = [path] + extra + ["--version"]
-            result = subprocess.run(cmd, capture_output=True, timeout=5, text=True)
-            if result.returncode == 0 and "Python" in (result.stdout or ""):
+            result = subprocess.run(cmd, capture_output=True, timeout=5, text=True, encoding="utf-8", errors="replace")
                 return (path, "auto-detected", extra)
         except (subprocess.TimeoutExpired, FileNotFoundError, PermissionError, OSError):
             continue
@@ -295,7 +294,7 @@ def _query_resolved_version(interp: str, extra_args: list[str]) -> tuple[str | N
     """
     try:
         cmd = [interp] + extra_args + ["--version"]
-        result = subprocess.run(cmd, capture_output=True, timeout=10, text=True)
+        result = subprocess.run(cmd, capture_output=True, timeout=10, text=True, encoding="utf-8", errors="replace")
         if result.returncode != 0:
             return (None, None)
         output = (result.stdout or "").strip() or (result.stderr or "").strip()
@@ -317,7 +316,7 @@ def _query_resolved_package(interp: str, extra_args: list[str], package_name: st
     """
     try:
         cmd = [interp] + extra_args + ["-m", "pip", "show", package_name]
-        result = subprocess.run(cmd, capture_output=True, timeout=15, text=True)
+        result = subprocess.run(cmd, capture_output=True, timeout=15, text=True, encoding="utf-8", errors="replace")
         if result.returncode != 0:
             return None
         output = (result.stdout or "").strip()
@@ -345,7 +344,7 @@ def _query_resolved_module(interp: str, extra_args: list[str], module_name: str)
     )
     try:
         cmd = [interp] + extra_args + ["-c", script]
-        result = subprocess.run(cmd, capture_output=True, timeout=15, text=True)
+        result = subprocess.run(cmd, capture_output=True, timeout=15, text=True, encoding="utf-8", errors="replace")
         if result.returncode != 0:
             return None
         output = (result.stdout or "").strip()