@luffysolution/omnischolar-pi 0.1.0 → 0.1.2

package/docs/RESEARCH.md

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+# 文献、Zotero 与 PDF
+
+[English](RESEARCH.en.md)
+
+## 文献检索
+
+| 工具 | 用途 |
+|---|---|
+| `research_sources` | 查看已启用的数据源和可用功能 |
+| `literature_search` | 检索论文，可限制年份、类型和开放获取状态 |
+| `literature_get` | 按 DOI、PMID/PMCID、arXiv ID 或数据源 ID 获取详情 |
+| `literature_graph` | 查询参考文献、施引文献或推荐论文 |
+| `journal_metrics` | 查询已支持的期刊指标 |
+| `literature_fulltext` | 查找合法全文地址，或将允许访问的文件保存到输出目录 |
+
+各数据源侧重点不同：
+
+- Semantic Scholar 和 OpenAlex 适合跨学科检索与引用关系。
+- PubMed/PMC 适合生物医学文献，PMC 还能提供带许可信息的开放全文。
+- arXiv 保留预印本标识符和版本信息。
+- Crossref 适合核对 DOI 注册元数据。
+- Unpaywall 用于查找开放获取版本，不绕过订阅或访问控制。
+- easyScholar 提供当前接口支持的期刊指标。
+- Ai4Scholar 还可查询 Google Scholar、Google Patents、作者、数据集和期刊信息，部分调用会消耗额度。
+
+检索时先用较小的 `limit`。优先按 DOI 去重；没有 DOI 时，再比较标题、年份和第一作者。标题相似只能用于筛选，不能代替正文证据。
+
+遇到 HTTP 429 时，OmniScholar 会返回限流信息。等待服务商给出的时间后再试，或改用支持同一查询的数据源。不要连续提交相同请求。
+
+## Zotero
+
+OmniScholar 只连接本机 Zotero API：
+
+```text
+http://127.0.0.1:23119/api
+```
+
+需要在 Zotero 中开启“允许其他应用程序与 Zotero 通信”，并保持 Zotero Desktop 运行。
+
+| 工具 | 可读取内容 |
+|---|---|
+| `zotero_collections` | 收藏夹及其条目 |
+| `zotero_search` | 文献条目、笔记、批注和附件 |
+| `zotero_item` | 单个条目或聚合后的论文视图 |
+
+聚合视图可包含书目信息、笔记、批注、附件信息、索引文本和本地 PDF 路径。OmniScholar 不会创建、修改、移动、加标签或删除 Zotero 数据。
+
+Zotero 笔记和批注属于个人阅读记录，不应当作论文原文证据。需要引用论文结论时，仍要核对原文。
+
+## MinerU 解析
+
+`omnischolar_parse` 检查 PDF 文件、计算 SHA-256，并使用 MinerU 返回正文、公式、表格和图片。解析结果会缓存；同一文件和解析设置再次调用时可直接命中缓存。
+
+上传必须同时得到两次确认：
+
+1. 配置中的 `mineru.allowExternalUpload` 为 `true`；
+2. 本次 `omnischolar_parse` 调用中的 `allowExternalUpload` 为 `true`。
+
+OmniScholar 不会自动把 Zotero 附件上传到 MinerU。应先确认具体条目和文件，再单独批准上传。`force` 会重新解析并产生一次新上传，因此也需要新的授权。
+
+下载的 MinerU 压缩包会在解压前检查路径、符号链接、文件数量和展开大小。检查失败时不写入输出目录。
+
+## 引用
+
+引用工作分为两步：先确认来源是否支持论点，再格式化书目信息。
+
+1. 用 `literature_search` 和 `literature_get` 查找来源。
+2. 核对 DOI、PMID、arXiv ID、标题、作者和年份。
+3. 阅读与论点相关的正文段落。
+4. 使用 `ai4scholar_citation_candidates` 补充候选时，先确认付费调用。
+5. 只对已核对的记录使用 `ai4scholar_cite`。
+
+格式正确的参考文献不代表论点已经得到支持。Ai4Scholar 的 Google Scholar 引用格式化目前可能缺少接口要求的结果 ID；遇到 `blocked` 时，不要自行拼接 ID。
+
+## 保存到 Markdown 或 Obsidian
+
+`omnischolar_sync` 会先给出计划，再写入 `output.rootDirectory`。该目录可以是普通文件夹，也可以位于 Obsidian Vault 中。
+
+同步会区分新建、无需更新、元数据变化、解析变化、渲染变化、文件缺失、冲突、排除和中断恢复。仅修复元数据、渲染或中断事务时不会上传 PDF。
+
+若已生成的 Markdown 被手工修改，默认策略会保留现有文件，并把新版本写入 `.conflicts/`。检查两份内容后再决定如何合并。
+
+首次写入真实 Vault 前，可先把 `output.rootDirectory` 指向临时目录，确认目录名、Markdown 和图片路径符合预期。

package/docs/TOOLS.en.md

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+# Tool list
+
+[简体中文](TOOLS.md)
+
+Tool and capability names match the values returned to agents.
+
+| Tool | Group | Capabilities | Side effects | Network | Credentials | Cost |
+|---|---|---|---|---:|---|---|
+| `omnischolar_status` | runtime | `runtime.status` | none | no | none | free |
+| `omnischolar_capabilities` | runtime | `runtime.capabilities` | none | no | none | free |
+| `research_sources` | literature | `literature.sources` | none | no | none | free |
+| `literature_search` | literature | `literature.search` | none | yes | none | free |
+| `literature_get` | literature | `literature.lookup` | none | yes | none | free |
+| `literature_graph` | literature | `literature.references`, `literature.citations`, `literature.recommendations` | none | yes | none | free |
+| `journal_metrics` | literature | `journal.metrics` | none | yes | none | free |
+| `literature_fulltext` | literature | `fulltext.resolve`, `fulltext.fetch` | filesystem | yes | none | free |
+| `zotero_collections` | zotero | `zotero.collections` | none | yes | none | free |
+| `zotero_search` | zotero | `zotero.search` | none | yes | none | free |
+| `zotero_item` | zotero | `zotero.item`, `zotero.aggregate` | none | yes | none | free |
+| `omnischolar_parse` | parsing | `pdf.parse`, `sync.publish` | external-upload | yes | mineru | metered |
+| `omnischolar_sync` | parsing | `sync.plan`, `sync.apply`, `sync.recovery` | filesystem | yes | none | free |
+| `ai4scholar_search` | ai4scholar | `ai4scholar.search` | paid | yes | ai4scholar | paid |
+| `ai4scholar_paper` | ai4scholar | `ai4scholar.paper` | paid | yes | ai4scholar | paid |
+| `ai4scholar_author` | ai4scholar | `ai4scholar.author` | paid | yes | ai4scholar | paid |
+| `ai4scholar_batch` | ai4scholar | `ai4scholar.batch` | paid | yes | ai4scholar | paid |
+| `ai4scholar_recommend` | ai4scholar | `ai4scholar.recommend` | paid | yes | ai4scholar | paid |
+| `ai4scholar_cite` | citation | `citation.format` | paid | yes | ai4scholar | paid |
+| `ai4scholar_snippets` | ai4scholar | `ai4scholar.snippets` | paid | yes | ai4scholar | paid |
+| `ai4scholar_credits` | ai4scholar | `ai4scholar.credits` | none | yes | ai4scholar | free |
+| `ai4scholar_dataset` | ai4scholar | `ai4scholar.dataset` | paid | yes | ai4scholar | paid |
+| `ai4scholar_journal` | ai4scholar | `ai4scholar.journal` | paid | yes | ai4scholar | paid |
+| `ai4scholar_citation_candidates` | citation | `citation.candidates` | paid | yes | ai4scholar | paid |
+| `ai4scholar_figure` | media | `media.generate`, `media.edit`, `media.vectorize` | paid | yes | ai4scholar | paid |
+| `materials_capabilities` | materials | `materials.capabilities` | none | no | materials-project | free |
+| `materials_search` | materials | `materials.search` | none | yes | materials-project | free |
+| `materials_route_search` | materials | `materials.route-search` | none | yes | materials-project | free |
+| `materials_get` | materials | `materials.lookup` | none | yes | materials-project | free |
+| `materials_advanced` | materials | `materials.phase-diagram`, `materials.xrd` | none | yes | materials-project | free |
+| `materials_export` | materials | `materials.export` | filesystem | no | none | free |
+| `chemical_sources` | chemistry | `chemistry.sources` | none | no | none | free |
+| `chemical_search` | chemistry | `chemistry.search` | none | yes | cas | free |
+| `chemical_get` | chemistry | `chemistry.lookup` | none | yes | cas | free |
+| `omnischolar_image_models` | media | `media.models` | none | yes | none | free |
+| `omnischolar_image_generate` | media | `text-to-image`, `image-to-image`, `multi-reference` | paid | yes | none | paid |
+| `omnischolar_image_edit` | media | `media.edit`, `multi-reference` | paid | yes | none | paid |
+| `omnischolar_image_service` | media | `media.service` | none | yes | none | free |
+
+Arguments not declared in a tool's input schema are rejected.
+Paid or upload-capable tools require both configuration and per-call authorization.

package/docs/TOOLS.md

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+# 工具目录
+
+[English](TOOLS.en.md)
+
+工具名和功能标识保留英文，便于与 Agent 返回结果对照。
+
+| 工具 | 分组 | 功能 | 可能产生的操作 | 联网 | 所需凭据 | 费用类型 |
+|---|---|---|---|---:|---|---|
+| `omnischolar_status` | runtime | `runtime.status` | none | no | none | free |
+| `omnischolar_capabilities` | runtime | `runtime.capabilities` | none | no | none | free |
+| `research_sources` | literature | `literature.sources` | none | no | none | free |
+| `literature_search` | literature | `literature.search` | none | yes | none | free |
+| `literature_get` | literature | `literature.lookup` | none | yes | none | free |
+| `literature_graph` | literature | `literature.references`, `literature.citations`, `literature.recommendations` | none | yes | none | free |
+| `journal_metrics` | literature | `journal.metrics` | none | yes | none | free |
+| `literature_fulltext` | literature | `fulltext.resolve`, `fulltext.fetch` | filesystem | yes | none | free |
+| `zotero_collections` | zotero | `zotero.collections` | none | yes | none | free |
+| `zotero_search` | zotero | `zotero.search` | none | yes | none | free |
+| `zotero_item` | zotero | `zotero.item`, `zotero.aggregate` | none | yes | none | free |
+| `omnischolar_parse` | parsing | `pdf.parse`, `sync.publish` | external-upload | yes | mineru | metered |
+| `omnischolar_sync` | parsing | `sync.plan`, `sync.apply`, `sync.recovery` | filesystem | yes | none | free |
+| `ai4scholar_search` | ai4scholar | `ai4scholar.search` | paid | yes | ai4scholar | paid |
+| `ai4scholar_paper` | ai4scholar | `ai4scholar.paper` | paid | yes | ai4scholar | paid |
+| `ai4scholar_author` | ai4scholar | `ai4scholar.author` | paid | yes | ai4scholar | paid |
+| `ai4scholar_batch` | ai4scholar | `ai4scholar.batch` | paid | yes | ai4scholar | paid |
+| `ai4scholar_recommend` | ai4scholar | `ai4scholar.recommend` | paid | yes | ai4scholar | paid |
+| `ai4scholar_cite` | citation | `citation.format` | paid | yes | ai4scholar | paid |
+| `ai4scholar_snippets` | ai4scholar | `ai4scholar.snippets` | paid | yes | ai4scholar | paid |
+| `ai4scholar_credits` | ai4scholar | `ai4scholar.credits` | none | yes | ai4scholar | free |
+| `ai4scholar_dataset` | ai4scholar | `ai4scholar.dataset` | paid | yes | ai4scholar | paid |
+| `ai4scholar_journal` | ai4scholar | `ai4scholar.journal` | paid | yes | ai4scholar | paid |
+| `ai4scholar_citation_candidates` | citation | `citation.candidates` | paid | yes | ai4scholar | paid |
+| `ai4scholar_figure` | media | `media.generate`, `media.edit`, `media.vectorize` | paid | yes | ai4scholar | paid |
+| `materials_capabilities` | materials | `materials.capabilities` | none | no | materials-project | free |
+| `materials_search` | materials | `materials.search` | none | yes | materials-project | free |
+| `materials_route_search` | materials | `materials.route-search` | none | yes | materials-project | free |
+| `materials_get` | materials | `materials.lookup` | none | yes | materials-project | free |
+| `materials_advanced` | materials | `materials.phase-diagram`, `materials.xrd` | none | yes | materials-project | free |
+| `materials_export` | materials | `materials.export` | filesystem | no | none | free |
+| `chemical_sources` | chemistry | `chemistry.sources` | none | no | none | free |
+| `chemical_search` | chemistry | `chemistry.search` | none | yes | cas | free |
+| `chemical_get` | chemistry | `chemistry.lookup` | none | yes | cas | free |
+| `omnischolar_image_models` | media | `media.models` | none | yes | none | free |
+| `omnischolar_image_generate` | media | `text-to-image`, `image-to-image`, `multi-reference` | paid | yes | none | paid |
+| `omnischolar_image_edit` | media | `media.edit`, `multi-reference` | paid | yes | none | paid |
+| `omnischolar_image_service` | media | `media.service` | none | yes | none | free |
+
+未在输入 schema 中声明的参数会被拒绝。
+付费或上传工具必须同时通过配置开关和本次调用的显式授权。

package/host-configs/README.md

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+# Agent configuration files
+
+- Portable Agent Plugin and Codex: root `plugin.json`, `mcp.json`, and `skills/`
+- Claude Code: `.claude-plugin/plugin.json`, root `.mcp.json`, and `skills/`
+- Cursor: root Agent Plugin files plus `.cursor-plugin/plugin.json`
+- OpenCode: merge `opencode.jsonc` into the project or user OpenCode config
+- Hermes: merge `hermes.yaml` into `~/.hermes/config.yaml`
+- Pi: see `pi.md`; the npm Extension bridges the local MCP server
+- WorkBuddy/CodeBuddy: merge `workbuddy.json` into `~/.codebuddy/.mcp.json` or project `.mcp.json`
+
+All supported MCP entries start the local command `omnischolar mcp`. These files contain no provider credentials.

package/host-configs/hermes.yaml

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+mcp_servers:
+  omnischolar:
+    command: "omnischolar"
+    args: ["mcp"]
+    # Optional: restrict exposure with tools.include or tools.exclude.
+    # Inherit OMNISCHOLAR_* and provider environment variables from Hermes.

package/host-configs/opencode.jsonc

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+{
+  "$schema": "https://opencode.ai/config.json",
+  "mcp": {
+    "omnischolar": {
+      "type": "local",
+      "command": ["omnischolar", "mcp"],
+      "enabled": true,
+      "timeout": 10000
+    }
+  }
+}

package/host-configs/pi.md

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+# Pi
+
+OmniScholar uses the npm-published `@luffysolution/omnischolar-pi` Extension to bridge its local MCP server into Pi. The full installer also copies Skills to `.pi/agent/skills` for user scope or `.pi/skills` for project scope.
+
+```sh
+omnischolar install pi
+# or install only the Extension with Pi's package manager
+pi install npm:@luffysolution/omnischolar-pi
+```
+
+The Extension starts `omnischolar mcp`, discovers the server's tools, forwards calls and cancellation signals, and closes the MCP client when the Pi session ends.
+
+`omnischolar mcp install pi` remains `manual_required` because Pi uses an Extension instead of a native MCP settings file. Use the full `omnischolar install pi` command.

package/host-configs/workbuddy.json

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+{
+  "mcpServers": {
+    "omnischolar": {
+      "type": "stdio",
+      "command": "omnischolar",
+      "args": ["mcp"],
+      "description": "OmniScholar research tools"
+    }
+  }
+}

package/host-configs/workbuddy.md

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+# Tencent WorkBuddy / CodeBuddy
+
+WorkBuddy/CodeBuddy CLI and IDE support local stdio MCP servers. Copy [`workbuddy.json`](workbuddy.json) into the MCP editor, or merge it into one of the documented files:
+
+- User scope: `~/.codebuddy/.mcp.json`
+- Project scope: `.mcp.json`
+
+The installer can write the same entry:
+
+```sh
+omnischolar install workbuddy
+omnischolar install workbuddy --scope project
+```
+
+The official documentation does not define a portable WorkBuddy Skills directory, so the Skills component remains manual.
+
+Official references checked on 2026-09-10:
+
+- <https://www.workbuddy.ai/docs/cli/mcp>
+- <https://www.workbuddy.ai/docs/ide/User-guide/MCP>

package/omnischolar.config.example.json

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+{
+  "schemaVersion": 1,
+  "runtime": {
+    "cacheDirectory": ".omnischolar/cache",
+    "python": "python",
+    "logLevel": "info",
+    "maxOutputBytes": 51200,
+    "maxOutputLines": 2000,
+    "maxResponseBytes": 16777216,
+    "requestTimeoutSeconds": 30,
+    "workspaceRoots": ["."]
+  },
+  "tools": {
+    "groups": {
+      "literature": true,
+      "ai4scholar": true,
+      "zotero": true,
+      "parsing": true,
+      "citation": true,
+      "materials": true,
+      "chemistry": true,
+      "media": true
+    },
+    "disabled": []
+  },
+  "defaults": {
+    "language": "en",
+    "citationStyle": "apa",
+    "literatureLimit": 20,
+    "preferredLiteratureProviders": ["semantic-scholar", "openalex", "crossref"],
+    "defaultImageProvider": "openai"
+  },
+  "research": {
+    "fallback": true,
+    "maxPages": 10,
+    "cacheTtlSeconds": 3600,
+    "providers": {
+      "semantic-scholar": {
+        "enabled": true,
+        "apiKeyEnv": "OMNISCHOLAR_SEMANTIC_SCHOLAR_API_KEY",
+        "maxPages": 10
+      },
+      "openalex": {
+        "enabled": true,
+        "email": "researcher@example.edu",
+        "maxPages": 10
+      },
+      "pubmed": {
+        "enabled": true,
+        "apiKeyEnv": "OMNISCHOLAR_NCBI_API_KEY",
+        "email": "researcher@example.edu",
+        "tool": "omnischolar",
+        "maxPages": 10
+      },
+      "arxiv": {
+        "enabled": true,
+        "maxPages": 10
+      },
+      "crossref": {
+        "enabled": true,
+        "email": "researcher@example.edu",
+        "maxPages": 10
+      },
+      "unpaywall": {
+        "enabled": false,
+        "email": "researcher@example.edu",
+        "maxPages": 10
+      },
+      "easyscholar": {
+        "enabled": false,
+        "apiKeyEnv": "OMNISCHOLAR_EASYSCHOLAR_API_KEY",
+        "maxPages": 5
+      }
+    }
+  },
+  "ai4scholar": {
+    "enabled": false,
+    "baseUrl": "https://ai4scholar.net",
+    "apiKeyEnv": "OMNISCHOLAR_AI4SCHOLAR_API_KEY",
+    "timeoutSeconds": 60,
+    "maxResponseBytes": 16777216,
+    "allowPaid": false
+  },
+  "zotero": {
+    "enabled": true,
+    "baseUrl": "http://127.0.0.1:23119/api",
+    "maxItems": 500
+  },
+  "mineru": {
+    "enabled": false,
+    "baseUrl": "https://mineru.net/api/v4",
+    "lightweightBaseUrl": "https://mineru.net/api/v1/agent",
+    "apiKeyEnv": "OMNISCHOLAR_MINERU_API_KEY",
+    "model": "pipeline",
+    "cacheDirectory": ".omnischolar/mineru",
+    "pollIntervalSeconds": 2,
+    "pollTimeoutSeconds": 600,
+    "maxPdfBytes": 209715200,
+    "allowExternalUpload": false,
+    "allowLightweightFallback": false
+  },
+  "data": {
+    "materialsProject": {
+      "enabled": false,
+      "baseUrl": "https://api.materialsproject.org",
+      "apiKeyEnv": "OMNISCHOLAR_MATERIALS_PROJECT_API_KEY",
+      "maxPages": 10
+    },
+    "casCommonChemistry": {
+      "enabled": false,
+      "apiKeyEnv": "OMNISCHOLAR_CAS_API_KEY",
+      "baseUrl": null,
+      "contractFile": null
+    }
+  },
+  "media": {
+    "allowExternalUpload": false,
+    "allowPaid": false,
+    "maxInputBytes": 26214400,
+    "maxArtifactBytes": 52428800,
+    "providers": {
+      "openai": {
+        "enabled": false,
+        "apiKeyEnv": "OMNISCHOLAR_OPENAI_API_KEY",
+        "baseUrl": "https://api.openai.com/v1",
+        "models": {
+          "gpt-image-1": {
+            "capabilities": ["text-to-image", "image-to-image", "edit", "multi-reference"],
+            "paid": true
+          }
+        },
+        "options": {}
+      },
+      "google": {
+        "enabled": false,
+        "apiKeyEnv": "OMNISCHOLAR_GEMINI_API_KEY",
+        "baseUrl": "https://generativelanguage.googleapis.com/v1beta",
+        "models": {},
+        "options": {}
+      },
+      "vertex": {
+        "enabled": false,
+        "apiKeyEnv": "OMNISCHOLAR_VERTEX_ACCESS_TOKEN",
+        "project": "your-project",
+        "location": "us-central1",
+        "models": {},
+        "options": {}
+      },
+      "xai": {
+        "enabled": false,
+        "apiKeyEnv": "OMNISCHOLAR_XAI_API_KEY",
+        "baseUrl": "https://api.x.ai/v1",
+        "models": {},
+        "options": {}
+      },
+      "fal": {
+        "enabled": false,
+        "apiKeyEnv": "OMNISCHOLAR_FAL_API_KEY",
+        "baseUrl": "https://fal.run",
+        "models": {},
+        "options": {}
+      },
+      "dashscope": {
+        "enabled": false,
+        "apiKeyEnv": "OMNISCHOLAR_DASHSCOPE_API_KEY",
+        "baseUrl": "https://your-workspace.cn-beijing.maas.aliyuncs.com/api/v1",
+        "models": {},
+        "options": {
+          "workspace": "your-workspace"
+        }
+      },
+      "qwen-cloud": {
+        "enabled": false,
+        "apiKeyEnv": "OMNISCHOLAR_QWEN_API_KEY",
+        "baseUrl": "https://your-workspace.ap-southeast-1.maas.aliyuncs.com/api/v1",
+        "models": {},
+        "options": {
+          "workspace": "your-workspace"
+        }
+      },
+      "atlas": {
+        "enabled": false,
+        "apiKeyEnv": "OMNISCHOLAR_ATLAS_API_KEY",
+        "baseUrl": "https://your-atlas-provider.example/v1",
+        "models": {},
+        "options": {}
+      },
+      "custom": {
+        "enabled": false,
+        "apiKeyEnv": "OMNISCHOLAR_CUSTOM_IMAGE_API_KEY",
+        "baseUrl": "https://images.example.edu/v1",
+        "models": {
+          "explicit-model-id": {
+            "capabilities": ["text-to-image"],
+            "paid": true
+          }
+        },
+        "options": {
+          "generationEndpoint": "images/generations",
+          "editEndpoint": "images/edits"
+        }
+      }
+    }
+  },
+  "sync": {
+    "namespace": null,
+    "cacheDirectory": ".omnischolar/sync",
+    "conflictPolicy": "preserve-local",
+    "recovery": true,
+    "backup": true,
+    "avoidUnnecessaryParse": true
+  },
+  "output": {
+    "rootDirectory": "omnischolar-output",
+    "conflictDirectory": ".conflicts",
+    "safeWrites": true
+  }
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@luffysolution/omnischolar-pi",
-  "version": "0.1.0",
+  "version": "0.1.2",
   "description": "Pi MCP bridge for the OmniScholar research toolkit",
   "type": "module",
   "license": "MIT",
@@ -29,7 +29,14 @@
   "files": [
     "pi-extension/dist",
     "README.md",
-    "LICENSE"
+    "README.zh-CN.md",
+    "LICENSE",
+    "PRIVACY.md",
+    "TERMS.md",
+    "THIRD_PARTY_NOTICES.md",
+    "omnischolar.config.example.json",
+    "docs",
+    "host-configs"
   ],
   "pi": {
     "extensions": [

package/pi-extension/dist/index.js

@@ -1,7 +1,7 @@
 import { Client } from "@modelcontextprotocol/sdk/client/index.js";
 import { StdioClientTransport } from "@modelcontextprotocol/sdk/client/stdio.js";
 import { Type } from "typebox";
-const CLIENT_INFO = { name: "omnischolar-pi", version: "0.1.0" };
+const CLIENT_INFO = { name: "omnischolar-pi", version: "0.1.2" };
 export function resultText(result) {
     return result.content
         .map((item) => {