fix(cli): use scievolve and update repository links

Author: chraodo

README.md

@@ -29,7 +29,7 @@ ScienceEvolve is the fully autoresearch framework in paper [Rethinking Scientifi
 
 [![ScienceEvolve SDK / CLI](docs/readme/badges/sdk-cli.svg)](#quick-start) — **This repository.** Run workflows from TypeScript or the command line and embed research in your own services. See the [SDK examples](example/README.md) and [Web / SDK comparison](sdk/docs/main-sdk-parity-zh.md) (Chinese).
 
-[![ScienceEvolve Web / Server](docs/readme/badges/web-server.svg)](https://github.com/fnlp-agentRL/SCION-AR/tree/main) — **Web / Server entry.** Compose Agents visually, connect model gateways, manage research projects, and inspect traces and delivered files.
+[![ScienceEvolve Web / Server](docs/readme/badges/web-server.svg)](https://github.com/OpenMOSS/ScienceEvolve-server) — **Web / Server entry.** Compose Agents visually, connect model gateways, manage research projects, and inspect traces and delivered files.
 
 ## Your research team, one workflow
 
@@ -127,14 +127,14 @@ You need **Node.js 24+**, **npm 10+**, Git to clone the source, and a model gate
 
 ### 1. Install the SDK and CLI
 
-Copy this branch's HTTPS clone address from **Code → HTTPS**, replace `REPOSITORY_URL`, and run:
+Clone the repository's `main` branch and install:
 
 ```sh
-git clone --branch feat/sdk-only-v0.1.1 --single-branch REPOSITORY_URL ScienceEvolve
+git clone --branch main --single-branch https://github.com/OpenMOSS/ScienceEvolve.git ScienceEvolve
 cd ScienceEvolve
 npm ci
 npm run install:cli
-scienceevolve --help
+scievolve --help
 ```
 
 Keep this terminal in the repository root. Create an empty task directory, such as `/absolute/todo-project`, and choose a separate absolute `/absolute/scienceevolve-data` directory for runtime state. Replace these paths in the commands below; neither directory may contain the other.
@@ -155,8 +155,8 @@ Save the following as `reasoning.json` in the repository root. Replace `YOUR_MOD
 ```
 
 ```sh
-scienceevolve gateway add --data-dir /absolute/scienceevolve-data --name research --url https://YOUR_PROVIDER/v1 --protocol chat-completions --models YOUR_MODEL --default-model YOUR_MODEL --key-env MODEL_API_KEY --reasoning-file reasoning.json
-scienceevolve gateway test GATEWAY_ID --data-dir /absolute/scienceevolve-data --model YOUR_MODEL --harness pi --reasoning-option high
+scievolve gateway add --data-dir /absolute/scienceevolve-data --name research --url https://YOUR_PROVIDER/v1 --protocol chat-completions --models YOUR_MODEL --default-model YOUR_MODEL --key-env MODEL_API_KEY --reasoning-file reasoning.json
+scievolve gateway test GATEWAY_ID --data-dir /absolute/scienceevolve-data --model YOUR_MODEL --harness pi --reasoning-option high
 ```
 
 Use the gateway ID returned by `gateway add` as `GATEWAY_ID`. Continue when the connection test passes. For other protocols, reasoning parameters, per-Agent models, or Codex native login, see the [model configuration guide](sdk/docs/main-cli-zh.md#部署与启动) (Chinese).
@@ -166,8 +166,8 @@ Use the gateway ID returned by `gateway add` as `GATEWAY_ID`. Continue when the
 Start with [software development and testing](example/02-software-development/workflow.json). It builds a Node.js Todo CLI, then tests and repairs it in the task directory:
 
 ```sh
-scienceevolve workflow validate example/02-software-development/workflow.json
-scienceevolve start example/02-software-development/workflow.json example/02-software-development/requirement.txt --data-dir /absolute/scienceevolve-data --workspace /absolute/todo-project --gateway GATEWAY_ID --model YOUR_MODEL --harness pi
+scievolve workflow validate example/02-software-development/workflow.json
+scievolve start example/02-software-development/workflow.json example/02-software-development/requirement.txt --data-dir /absolute/scienceevolve-data --workspace /absolute/todo-project --gateway GATEWAY_ID --model YOUR_MODEL --harness pi
 ```
 
 The CLI streams events and prints the run ID and final status. When the status is `completed`, inspect the source, tests, and usage instructions in your task directory, with execution records under `development/`. To pause, press **Ctrl+C**, wait for shutdown, and use the printed resume command with the same data directory.

README_zh-CN.md

@@ -1,4 +1,4 @@
-<h1 align="center">ScienceEvolve SDK</h1>
+<h1 align="center">ScienceEvolve</h1>
 
 <p align="center">
   <strong>在一个工作流里，组织、运行和持续改进多 Agent 科研任务。</strong>
@@ -21,15 +21,15 @@
 
 ---
 
-ScienceEvolve 将研究、实验、编码和评审连接成可编程工作流。你可以组建自己的 Agent 团队，查看真实执行轨迹，让团队根据评估反馈改进任务，也可以授权 Main 调整工作流本身。
+ScienceEvolve 是论文 [Rethinking Scientific Discovery in the Agentic Era](https://arxiv.org/abs/2607.03863) 中的全自动科研框架。你可以组建自己的 Agent 团队，查看真实执行轨迹，让团队根据评估反馈改进任务，也可以授权 Main 调整工作流本身。
 
 <a id="sdk"></a>
 
 **🧩 ScienceEvolve 的两种使用方式** — 同一套工作流语义，按你的工作方式选择入口。
 
 [![ScienceEvolve SDK / CLI](docs/readme/badges/sdk-cli.svg)](#quick-start) — **当前仓库**。通过 TypeScript 或命令行运行工作流，将研究流程接入自己的代码与服务。参见 [SDK 示例](example/README.md)与 [Web / SDK 对照](sdk/docs/main-sdk-parity-zh.md)。
 
-[![ScienceEvolve Web / Server](docs/readme/badges/web-server.svg)](https://github.com/fnlp-agentRL/SCION-AR/tree/main) — **Web / Server 入口**。在网页中编排 Agent、连接模型网关、管理研究项目，查看轨迹与交付文件。
+[![ScienceEvolve Web / Server](docs/readme/badges/web-server.svg)](https://github.com/OpenMOSS/ScienceEvolve-server) — **Web / Server 入口**。在网页中编排 Agent、连接模型网关、管理研究项目，查看轨迹与交付文件。
 
 ## 组建自己的科研 Agent 团队
 
@@ -127,14 +127,14 @@ System Runtime 保存项目状态、已完成进度和执行轨迹。可恢复
 
 ### 1. 安装 SDK 与 CLI
 
-从当前分支的 **Code → HTTPS** 复制仓库地址，替换 `REPOSITORY_URL` 后执行：
+克隆仓库的 `main` 分支并安装：
 
 ```sh
-git clone --branch feat/sdk-only-v0.1.1 --single-branch REPOSITORY_URL ScienceEvolve
+git clone --branch main --single-branch https://github.com/OpenMOSS/ScienceEvolve.git ScienceEvolve
 cd ScienceEvolve
 npm ci
 npm run install:cli
-scienceevolve --help
+scievolve --help
 ```
 
 后续命令在仓库根目录执行。新建一个空任务目录，例如 `/absolute/todo-project`，另选绝对路径 `/absolute/scienceevolve-data` 保存运行状态。将下面的路径替换为本机路径；两个目录分开且互不包含。
@@ -155,8 +155,8 @@ scienceevolve --help
 ```
 
 ```sh
-scienceevolve gateway add --data-dir /absolute/scienceevolve-data --name research --url https://YOUR_PROVIDER/v1 --protocol chat-completions --models YOUR_MODEL --default-model YOUR_MODEL --key-env MODEL_API_KEY --reasoning-file reasoning.json
-scienceevolve gateway test GATEWAY_ID --data-dir /absolute/scienceevolve-data --model YOUR_MODEL --harness pi --reasoning-option high
+scievolve gateway add --data-dir /absolute/scienceevolve-data --name research --url https://YOUR_PROVIDER/v1 --protocol chat-completions --models YOUR_MODEL --default-model YOUR_MODEL --key-env MODEL_API_KEY --reasoning-file reasoning.json
+scievolve gateway test GATEWAY_ID --data-dir /absolute/scienceevolve-data --model YOUR_MODEL --harness pi --reasoning-option high
 ```
 
 将 `gateway add` 返回的网关 ID 填入 `GATEWAY_ID`，连接测试通过后继续。其他协议、推理参数、逐 Agent 模型绑定和 Codex 原生登录见[模型配置指南](sdk/docs/main-cli-zh.md#部署与启动)。
@@ -166,8 +166,8 @@ scienceevolve gateway test GATEWAY_ID --data-dir /absolute/scienceevolve-data --
 先运行[软件开发与测试](example/02-software-development/workflow.json)：在任务目录中实现 Node.js 待办 CLI，并完成测试和修复。
 
 ```sh
-scienceevolve workflow validate example/02-software-development/workflow.json
-scienceevolve start example/02-software-development/workflow.json example/02-software-development/requirement.txt --data-dir /absolute/scienceevolve-data --workspace /absolute/todo-project --gateway GATEWAY_ID --model YOUR_MODEL --harness pi
+scievolve workflow validate example/02-software-development/workflow.json
+scievolve start example/02-software-development/workflow.json example/02-software-development/requirement.txt --data-dir /absolute/scienceevolve-data --workspace /absolute/todo-project --gateway GATEWAY_ID --model YOUR_MODEL --harness pi
 ```
 
 CLI 持续输出事件，并打印 run ID 和最终状态。状态为 `completed` 后，在任务目录查看源码、测试和使用说明，执行记录位于 `development/`。需要暂停时按 **Ctrl+C**，等待退出，再用打印出的恢复命令和原数据目录继续。

docs/sdk/science-rsi-feasibility.md

@@ -67,7 +67,7 @@ python -m unittest discover -s example/tests -v
 # SDK真实配置加载、完整Skill文件暂存、移植路径和TODO互斥
 npm test -- --run tests/research-examples.test.ts
 # 按模板重复CLI校验；不调用模型
-scienceevolve workflow validate example/aris/workflow.json
+scievolve workflow validate example/aris/workflow.json
 ```
 
 Python测试需numpy、scipy、absl-py、PyPDF2；新增Biomni原子执行测试还需可导入A1的LangChain/LangGraph核心环境，缺依赖时测试显式skip而不是报告已覆盖。新增检查实际持久REPL、自批评、过期prompt、文件假设池、Elo与幂等、真实本地HTTP/PDF回读。完整E1/数据和远程科研环境另行部署。此前额外运行固定Anti-Autoresearch的9个确定性eval fixture（7个注入缺陷全部检出、clean无误报）。这些均未调用审计LLM。覆盖原FunSearch默认参数/同RNG prompt/四样本/幂等恢复/失败候选/弱半岛重置、原ARIS门槛及过期证据、真实Git回退、原论文评分公式、原Meta-Harness冻结集合与缺测试时拒绝完成、Robin五轨迹聚合门槛、上游文件哈希。SDK测试验证Skill复制后原脚本及资源仍存在。SciAgents真实图工具、ARIS所有科研分支、Lab完整实验、Robin远程数据分析等仍需实际环境端到端验收，离线检查不覆盖它们的科学有效性。

example/README.md

@@ -35,8 +35,8 @@
 ```sh
 npm ci
 npm run install:cli
-scienceevolve workflow validate example/kosmos/workflow.json
-scienceevolve start example/kosmos/workflow.json example/kosmos/requirement.txt \
+scievolve workflow validate example/kosmos/workflow.json
+scievolve start example/kosmos/workflow.json example/kosmos/requirement.txt \
   --data-dir /absolute/run-data --workspace /absolute/task \
   --gateway-bindings /absolute/bindings.json
 ```

package-lock.json

@@ -4,7 +4,7 @@
 
 Run multi-Agent research workflows from Node.js or the command line. The SDK supports review loops, Git collaboration, workflow evolution, persistent state, and recovery.
 
-The [repository overview](https://github.com/fnlp-agentRL/SCION-AR/blob/feat/sdk-only-v0.1.1/README.md) covers the quick start, diagrams, 23 source workflows, and upstream acknowledgements.
+The [repository overview](https://github.com/OpenMOSS/ScienceEvolve/blob/main/README.md) covers the quick start, diagrams, 23 source workflows, and upstream acknowledgements.
 
 ## Installation and Skill
 
@@ -30,8 +30,8 @@ The SDK bundles pi; install Codex, Claude Code, DSH, or [Hermes](docs/hermes-zh.
 Choose a dedicated absolute `dataDir`, then [add and test a model gateway](docs/main-cli-zh.md#部署与启动) in that directory. Set each Agent's model, Harness, and reasoning option in your workflow. Use the returned gateway ID when starting:
 
 ```sh
-scienceevolve workflow validate /absolute/workflow.json
-scienceevolve start /absolute/workflow.json /absolute/requirement.txt --data-dir /absolute/scienceevolve-data --workspace /absolute/task-project --gateway GATEWAY_ID
+scievolve workflow validate /absolute/workflow.json
+scievolve start /absolute/workflow.json /absolute/requirement.txt --data-dir /absolute/scienceevolve-data --workspace /absolute/task-project --gateway GATEWAY_ID
 ```
 
 The task directory must exist and be separate from `dataDir`. Git-off runs directly in it; Git-on uses isolated worktrees and delivers the integrated result back. Press Ctrl+C to pause, wait for shutdown, then use the printed resume command. Keep one SDK host per data directory.

sdk/README.md

@@ -4,7 +4,7 @@
 
 通过 Node.js 或命令行运行多 Agent 科研工作流，支持评审循环、Git 协作、流程演化、状态持久化与中断恢复。
 
-[源码仓库首页](https://github.com/fnlp-agentRL/SCION-AR/blob/feat/sdk-only-v0.1.1/README_zh-CN.md)提供快速开始、功能图、23 个源码工作流和上游致谢。
+[源码仓库首页](https://github.com/OpenMOSS/ScienceEvolve/blob/main/README_zh-CN.md)提供快速开始、功能图、23 个源码工作流和上游致谢。
 
 ## 安装与 Skill
 
@@ -30,8 +30,8 @@ pi 随包提供；Codex、Claude Code、DSH 和 [Hermes](docs/hermes-zh.md) 按
 选择专用的绝对 `dataDir`，先在该目录[添加并测试模型网关](docs/main-cli-zh.md#部署与启动)，再为 workflow 中的 Agent 配置模型、Harness 和推理档位。启动时使用返回的网关 ID：
 
 ```sh
-scienceevolve workflow validate /absolute/workflow.json
-scienceevolve start /absolute/workflow.json /absolute/requirement.txt --data-dir /absolute/scienceevolve-data --workspace /absolute/task-project --gateway GATEWAY_ID
+scievolve workflow validate /absolute/workflow.json
+scievolve start /absolute/workflow.json /absolute/requirement.txt --data-dir /absolute/scienceevolve-data --workspace /absolute/task-project --gateway GATEWAY_ID
 ```
 
 任务目录须已存在，并与 `dataDir` 分开且互不包含。Git-off 在原目录执行；Git-on 使用隔离 worktree，集成后回写结果。按 Ctrl+C 暂停，等待退出，再使用打印出的命令恢复。同一个数据目录同时由一个 SDK 宿主持有。

sdk/README_zh-CN.md

@@ -3,7 +3,7 @@ import path from "node:path";
 
 export const mainHelp = `ScienceEvolve CLI — default main engine
 
-Usage: scienceevolve <command> [--engine main] --data-dir <absolute-dedicated-directory>
+Usage: scievolve <command> [--engine main] --data-dir <absolute-dedicated-directory>
        [--runtime-config <deployment-json>]
 
   harnesses
@@ -113,7 +113,7 @@ export async function runMainCli(positionals, options, services = {}) {
     return /^[a-zA-Z0-9_./:-]+$/.test(value) ? value : "'" + value.replaceAll("'", process.platform === "win32" ? "''" : "'\"'\"'") + "'";
   }
   function resumeGuidance(id, dataDir) {
-    const args = ["scienceevolve", "run", "resume", id, "--engine", "main", "--data-dir", dataDir];
+    const args = ["scievolve", "run", "resume", id, "--engine", "main", "--data-dir", dataDir];
     if (options.has("runtime-config")) args.push("--runtime-config", path.resolve(required("runtime-config")));
     guidance(`任务已暂停，现场已保存：${id}\n恢复命令${process.platform === "win32" ? "（PowerShell）" : ""}：\n${args.map(shellArgument).join(" ")}`);
   }

sdk/cli/main-cli.mjs

@@ -16,7 +16,7 @@ const packageInfo = JSON.parse(await readFile(path.join(packageRoot, "package.js
 const harnessIds = ["codex", "pi", "dsh", "claude-code"];
 const help = `ScienceEvolve CLI ${packageInfo.version}
 
-Usage: scienceevolve <command> [arguments] [--runtime-config <file>] [--data-dir <absolute-directory>]
+Usage: scievolve <command> [arguments] [--runtime-config <file>] [--data-dir <absolute-directory>]
 
 Explicit legacy engine: --engine legacy. Without that flag the CLI uses main's
 kernel and a dedicated --data-dir. This help documents only the legacy fallback.
@@ -112,7 +112,7 @@ function shellArgument(value) {
 }
 
 function resumeGuidance(runId, options, dataDir) {
-  const args = ["scienceevolve", "run", "resume", runId, "--engine", "legacy", "--data-dir", dataDir];
+  const args = ["scievolve", "run", "resume", runId, "--engine", "legacy", "--data-dir", dataDir];
   if (options.has("runtime-config")) args.push("--runtime-config", path.resolve(options.get("runtime-config")));
   guidance(`\n任务已暂停，进度已保存：${runId}`, "32");
   guidance(`执行以下命令继续流程${process.platform === "win32" ? "（PowerShell）" : ""}：`, "36");