@hongmaple0820/med-scale-research-os 0.43.0

package/.scale/verification.json

@@ -0,0 +1,52 @@
+{
+  "version": 1,
+  "defaultProfile": "default",
+  "profiles": {
+    "default": {
+      "commands": {
+        "build": "npm run build",
+        "lint": "npm run lint",
+        "test": "npx vitest run --reporter=dot --testTimeout=30000"
+      },
+      "services": [
+        "med-scale-research-os"
+      ]
+    },
+    "productSmoke": {
+      "commands": {
+        "smoke": "powershell -ExecutionPolicy Bypass -File scripts/qa/product-smoke.ps1"
+      },
+      "services": [
+        "med-scale-research-os"
+      ]
+    }
+  },
+  "services": [
+    {
+      "name": "med-scale-research-os",
+      "path": ".",
+      "type": "node",
+      "required": true
+    }
+  ],
+  "exclude": [
+    "node_modules",
+    "dist",
+    "tmp",
+    "temp",
+    "coverage",
+    "test-results"
+  ],
+  "policy": {
+    "mode": "standard",
+    "optionalToolsWarnOnly": true,
+    "artifactGate": "warn",
+    "artifactGateLevels": [
+      "M",
+      "L",
+      "CRITICAL"
+    ],
+    "engineeringStandardsGate": "block",
+    "productSmokeGate": "warn"
+  }
+}

package/LICENSE

@@ -0,0 +1,15 @@
+MIT License
+
+Copyright (c) 2026 SCALE Engine Contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND.

package/README.en.md

@@ -0,0 +1,156 @@
+# MedSCALE Research OS
+
+MedSCALE Research OS is a local research operating system for medical research workflows. It connects target/disease research, literature review, medical fact checking, delivery package audit, memory seeding, learning-candidate review, and a researcher-facing dashboard into a verifiable evidence loop.
+
+> MedSCALE is for research workflow governance and evidence organization only. It is not clinical advice, medical diagnosis, treatment guidance, or a submission guarantee. Human expert review is required.
+
+Source: https://github.com/hongmaple0820/med-scale-research-os
+npm package: `@hongmaple0820/med-scale-research-os`
+Language: [Chinese](README.md) | [English](README.en.md)
+
+## Current State
+
+- Product name: **MedSCALE Research OS**
+- Main CLI: `medscale`
+- Local dashboard: `http://127.0.0.1:18766`
+- Medical execution kernel: `target-research-platform`
+- Memory provider: gbrain ready, agentmemory not enabled
+- Code/knowledge graph: Graphify ready, CodeGraph partial
+- MCP: MedSCALE server map exists; live health checks are still pending
+- Native doctor: PubMed/OpenAlex, package audit, figure refs, and token/cost deep checks are wired
+- Local visual setup guide: `medscale setup --visual --lang en`
+- Token/cost: local ledger, CLI record/report/ingest, usage envelopes, and 18766 panel are wired; delivery packaging automatically scans real medical usage artifacts
+- Planned gaps: post-publish npx verification, live MCP health, real external model-call replay verification
+
+## Quick Start
+
+Local development:
+
+```bash
+npm install
+npm run build
+npm run medscale -- doctor --json
+npm run medscale -- setup --lang en
+npm run medscale -- setup --visual --lang en
+npm run medscale -- dashboard
+```
+
+Run after build:
+
+```bash
+node dist/api/medscale.js doctor --json
+node dist/api/medscale.js setup --lang en
+node dist/api/medscale.js setup --visual --lang en
+node dist/api/medscale.js dashboard
+```
+
+Target entry after package publication:
+
+```bash
+npx -y @hongmaple0820/med-scale-research-os setup --lang en
+npx -y @hongmaple0820/med-scale-research-os setup --visual --lang en
+npx -y @hongmaple0820/med-scale-research-os doctor --json
+npx -y @hongmaple0820/med-scale-research-os dashboard
+```
+
+## Core Commands
+
+```bash
+medscale doctor --json
+medscale setup --lang zh
+medscale setup --lang en
+medscale setup --visual --lang en
+medscale os-plan --json
+medscale token report --json
+medscale token record --provider anthropic --medical-lane literature --usage-file usage.json --json
+medscale token ingest --target CDK4 --disease "breast cancer" --json
+medscale token ingest --file artifact-usage.json --provider anthropic --json
+medscale dashboard
+medscale memory-review approve --candidate-id <id> --json
+medscale memory-review reject --candidate-id <id> --json
+medscale memory-review stale --candidate-id <id> --json
+medscale memory-review restore --candidate-id <id> --json
+```
+
+## 18766 Researcher View
+
+The dashboard home card layer now shows:
+
+- manuscript quality gate
+- medical fact check
+- delivery ZIP / package audit
+- gbrain memory seed
+- learning candidate
+- Memory Brain review status
+- Token / Cost panel
+- MedSCALE Research OS runtime doctor
+- medical Prompt Studio templates
+
+The learning-candidate card supports four explicit review actions:
+
+- approve: promote to an active Memory Brain node
+- reject: mark as rejected
+- stale: mark as stale
+- restore: restore to candidate review state
+
+These actions write audit records to:
+
+- `.scale/memory/learning-candidates/<candidate>.review.json`
+- `.scale/memory/learning-candidates/<candidate>.review.md`
+
+## Medical Capabilities
+
+Configured MedSCALE skill domains:
+
+- `medicalLiteratureReview`
+- `medicalFactCheck`
+- `medicalEvidenceGrading`
+- `medicalStatisticalReview`
+- `medicalPackageAudit`
+- `medicalMemoryCurator`
+
+Configured MedSCALE MCP route ids:
+
+- `medical-literature`
+- `medical-fact-check`
+- `medical-memory-review`
+- `medical-package-audit`
+- `medical-evidence-manifest`
+
+## Cross-Platform Goal
+
+`medscale setup` returns explicit install and verification commands for:
+
+- Windows
+- macOS
+- Linux
+
+Third-party tools are not installed silently. Missing capabilities are reported as ready, partial, missing, or planned.
+
+## Verification
+
+Recommended minimum checks:
+
+```bash
+npm run typecheck
+npm run build
+npm run smoke:medscale-release
+npm test -- tests/memory/MemoryReview.test.ts tests/cli/targetCommands.test.ts tests/cli/medscaleCli.test.ts
+cd target-research-platform
+python -m pytest tests/test_deliverables.py
+```
+
+Recently verified:
+
+- MedSCALE release smoke: `medscale.release_smoke.v1 passed`
+- Dashboard deliverables tests: `25 passed`
+- Memory review CLI tests cover approve / reject / stale / restore
+- 18766 render smoke: Memory review buttons visible, no page errors
+
+## Repository Note
+
+This repository evolved from the general SCALE Engine governance kernel. Historical governance modules remain in source so MedSCALE can reuse workflow gates, skills, MCP, memory, and evidence structures. The medical research workflow user entrypoint is `medscale`; users should not need the `scale` CLI to run MedSCALE workflows.
+
+## License
+
+[MIT](LICENSE)

package/README.md

@@ -0,0 +1,156 @@
+# MedSCALE Research OS
+
+MedSCALE Research OS（MedSCALE 医研操作系统）是一个面向医学研究工作流的本地研究操作系统。它把靶点/疾病研究、文献评审、事实核查、交付包审计、记忆播种、learning candidate 审核和研究者 dashboard 组织成可验证、可复核、可沉淀的闭环。
+
+> MedSCALE 只用于研究工作流治理和证据组织，不提供临床诊断、治疗建议或投稿保证。所有医学结论都需要人类专家复核。
+
+源码仓库：https://github.com/hongmaple0820/med-scale-research-os
+npm 包名：`@hongmaple0820/med-scale-research-os`
+语言：[中文](README.md) | [English](README.en.md)
+
+## 当前状态
+
+- 产品名：**MedSCALE Research OS / MedSCALE 医研操作系统**
+- 主入口：`medscale`
+- 本地 dashboard：`http://127.0.0.1:18766`
+- 医学执行内核：`target-research-platform`
+- 记忆供应商：gbrain ready，agentmemory 未启用
+- 代码/知识图谱：Graphify ready，CodeGraph partial
+- MCP：已有 MedSCALE server map，live health 仍待深化
+- Native doctor：已纳入 PubMed/OpenAlex、package audit、figure refs、token/cost 深度检查
+- 已有本地可视化安装向导：`medscale setup --visual --lang zh`
+- Token/cost：本地账本、CLI record/report/ingest、usage envelope 和 18766 面板已接入；交付包会自动扫描真实医学 usage 产物
+- 待补能力：npm 首次发布后的 npx 验证、live MCP health、真实外部模型调用回放验证
+
+## 快速开始
+
+本地开发：
+
+```bash
+npm install
+npm run build
+npm run medscale -- doctor --json
+npm run medscale -- setup --lang zh
+npm run medscale -- setup --visual --lang zh
+npm run medscale -- dashboard
+```
+
+构建后直接运行：
+
+```bash
+node dist/api/medscale.js doctor --json
+node dist/api/medscale.js setup --lang zh
+node dist/api/medscale.js setup --visual --lang zh
+node dist/api/medscale.js dashboard
+```
+
+未来发布后目标入口：
+
+```bash
+npx -y @hongmaple0820/med-scale-research-os setup --lang zh
+npx -y @hongmaple0820/med-scale-research-os setup --visual --lang zh
+npx -y @hongmaple0820/med-scale-research-os doctor --json
+npx -y @hongmaple0820/med-scale-research-os dashboard
+```
+
+## 核心命令
+
+```bash
+medscale doctor --json
+medscale setup --lang zh
+medscale setup --lang en
+medscale setup --visual --lang zh
+medscale os-plan --json
+medscale token report --json
+medscale token record --provider anthropic --medical-lane literature --usage-file usage.json --json
+medscale token ingest --target CDK4 --disease "breast cancer" --json
+medscale token ingest --file artifact-usage.json --provider anthropic --json
+medscale dashboard
+medscale memory-review approve --candidate-id <id> --json
+medscale memory-review reject --candidate-id <id> --json
+medscale memory-review stale --candidate-id <id> --json
+medscale memory-review restore --candidate-id <id> --json
+```
+
+## 18766 研究者视图
+
+首页卡片层已经展示：
+
+- 论文质量门禁
+- 医学事实核查
+- 交付 ZIP / package audit
+- gbrain memory seed
+- learning candidate
+- Memory Brain review 状态
+- Token / Cost 面板
+- MedSCALE Research OS runtime doctor
+- 医学 Prompt Studio 模板
+
+learning candidate 卡片支持四个显式审核动作：
+
+- 批准：promote 为 active Memory Brain node
+- 拒绝：标记为 rejected
+- 标记过期：标记为 stale
+- 恢复复审：恢复为 candidate 状态
+
+这些动作会写入：
+
+- `.scale/memory/learning-candidates/<candidate>.review.json`
+- `.scale/memory/learning-candidates/<candidate>.review.md`
+
+## 医学专用能力
+
+已配置的 MedSCALE skill domains：
+
+- `medicalLiteratureReview`
+- `medicalFactCheck`
+- `medicalEvidenceGrading`
+- `medicalStatisticalReview`
+- `medicalPackageAudit`
+- `medicalMemoryCurator`
+
+已配置的 MedSCALE MCP route ids：
+
+- `medical-literature`
+- `medical-fact-check`
+- `medical-memory-review`
+- `medical-package-audit`
+- `medical-evidence-manifest`
+
+## 跨平台目标
+
+`medscale setup` 会按平台给出显式安装/验证命令，覆盖：
+
+- Windows
+- macOS
+- Linux
+
+第三方能力不会静默自动安装。缺失能力会进入 setup/doctor 的 ready、partial、missing、planned 状态矩阵。
+
+## 验证
+
+推荐最小验证：
+
+```bash
+npm run typecheck
+npm run build
+npm run smoke:medscale-release
+npm test -- tests/memory/MemoryReview.test.ts tests/cli/targetCommands.test.ts tests/cli/medscaleCli.test.ts
+cd target-research-platform
+python -m pytest tests/test_deliverables.py
+```
+
+当前已验证的关键结果：
+
+- MedSCALE release smoke：`medscale.release_smoke.v1 passed`
+- Dashboard deliverables tests：`25 passed`
+- Memory review CLI tests：approve / reject / stale / restore 已覆盖
+- 18766 页面渲染：Memory review 按钮可见，无页面错误
+
+## 仓库说明
+
+这个仓库从通用 SCALE Engine 治理内核演进而来。历史治理模块仍保留在源码中，供 MedSCALE 复用工程门禁、skills、MCP、记忆和证据结构；医学研究工作流的用户入口以 `medscale` 为准，不要求用户通过 `scale` CLI 运行医学流程。
+
+## License
+
+[MIT](LICENSE)

package/dist/adapters/AiderAdapter.d.ts

@@ -0,0 +1,22 @@
+import type { IAgentAdapter, AdapterConfig, InitResult, SettingsJson } from './ClaudeCodeAdapter.js';
+export declare class AiderAdapter implements IAgentAdapter {
+    readonly agentType = "aider";
+    private projectDir;
+    private scaleDir;
+    getSettingsPath(): string;
+    getKnowledgeDocPath(): string;
+    getSkillsDir(): string;
+    isInstalled(): boolean;
+    /**
+     * Generate settings as JSON (interface requirement)
+     * Aider uses YAML, so init() will convert this to YAML format
+     */
+    generateSettings(): SettingsJson;
+    mergeSettings(existing: SettingsJson): SettingsJson;
+    /**
+     * Convert SettingsJson to YAML format for Aider
+     */
+    private settingsToYaml;
+    generateKnowledgeDoc(projectName: string, techStack?: string[]): string;
+    init(config: AdapterConfig): Promise<InitResult>;
+}

package/dist/adapters/AiderAdapter.js

@@ -0,0 +1,262 @@
+// SCALE Engine — Aider Adapter
+// 生成 .aider.conf.yml + AIDER.md
+// Aider: 开源 AI 编码 CLI (https://github.com/Aider-AI/aider)
+import { existsSync, readFileSync, writeFileSync, mkdirSync } from 'node:fs';
+import { join } from 'node:path';
+import { logger } from '../core/logger.js';
+// ============================================================================
+// Aider Adapter
+// ============================================================================
+export class AiderAdapter {
+    constructor() {
+        this.agentType = 'aider';
+        this.projectDir = '.';
+        this.scaleDir = '.scale';
+    }
+    getSettingsPath() {
+        return join(this.projectDir, '.aider.conf.yml');
+    }
+    getKnowledgeDocPath() {
+        return join(this.projectDir, 'AIDER.md');
+    }
+    getSkillsDir() {
+        // Aider uses .aider/commands/ for custom commands
+        return join(this.projectDir, '.aider', 'commands');
+    }
+    isInstalled() {
+        return existsSync(join(this.projectDir, '.aider')) ||
+            existsSync(this.getSettingsPath());
+    }
+    /**
+     * Generate settings as JSON (interface requirement)
+     * Aider uses YAML, so init() will convert this to YAML format
+     */
+    generateSettings() {
+        return {
+            hooks: {
+                'pre-tool-use': [
+                    { matcher: 'Bash', command: 'scale gate pre-tool Bash --args-json "$ARGS" --session-id "$SESSION_ID"' },
+                    { matcher: 'Editor|ApplyFix', command: 'scale gate pre-tool Edit --args-json "$ARGS" --session-id "$SESSION_ID"' },
+                    { matcher: 'Create', command: 'scale gate pre-tool Write --args-json "$ARGS" --session-id "$SESSION_ID"' },
+                ],
+                'post-tool-use': [
+                    { matcher: 'Editor|ApplyFix', command: 'scale gate post-tool Edit --args-json "$ARGS" --exit-code "$EXIT_CODE" --session-id "$SESSION_ID"' },
+                    { matcher: 'Bash', command: 'scale gate post-tool Bash --args-json "$ARGS" --exit-code "$EXIT_CODE" --session-id "$SESSION_ID"' },
+                    { matcher: 'Create', command: 'scale gate post-tool Write --args-json "$ARGS" --exit-code "$EXIT_CODE" --session-id "$SESSION_ID"' },
+                ],
+                'exit': [
+                    { matcher: '', command: 'scale gate before-stop --session-id "$SESSION_ID"' },
+                ],
+            },
+            permissions: {
+                allow: ['scale:*'],
+            },
+        };
+    }
+    mergeSettings(existing) {
+        const generated = this.generateSettings();
+        const merged = { ...existing };
+        if (!merged.hooks)
+            merged.hooks = {};
+        for (const [hookType, entries] of Object.entries(generated.hooks)) {
+            if (!merged.hooks[hookType])
+                merged.hooks[hookType] = [];
+            for (const entry of entries) {
+                const alreadyExists = merged.hooks[hookType].some((e) => e.command.includes('scale '));
+                if (!alreadyExists) {
+                    merged.hooks[hookType].push(entry);
+                }
+            }
+        }
+        if (!merged.permissions)
+            merged.permissions = {};
+        if (!merged.permissions.allow)
+            merged.permissions.allow = [];
+        for (const perm of generated.permissions.allow) {
+            if (!merged.permissions.allow.includes(perm)) {
+                merged.permissions.allow.push(perm);
+            }
+        }
+        return merged;
+    }
+    /**
+     * Convert SettingsJson to YAML format for Aider
+     */
+    settingsToYaml(settings) {
+        const lines = [
+            '# Aider Configuration with SCALE Engine Integration',
+            '# https://github.com/Aider-AI/aider',
+            '',
+        ];
+        // Write hooks section
+        if (settings.hooks) {
+            for (const [hookType, entries] of Object.entries(settings.hooks)) {
+                lines.push(`${hookType}:`);
+                for (const entry of entries) {
+                    lines.push(`  - command: ${entry.command}`);
+                    if (entry.matcher) {
+                        lines.push(`    tools: ["${entry.matcher.replace(/\|/g, '", "')}"]`);
+                    }
+                }
+                lines.push('');
+            }
+        }
+        // Write permissions section
+        if (settings.permissions?.allow) {
+            lines.push('# Allow SCALE commands without confirmation');
+            lines.push('auto-commits: false');
+            lines.push('dirty-commits: true');
+            lines.push('');
+        }
+        // Write additional Aider-specific settings
+        lines.push('# Model settings (can be overridden)');
+        lines.push('model: auto');
+        lines.push('');
+        lines.push('# Read AIDER.md for project context');
+        lines.push('read: AIDER.md');
+        return lines.join('\n');
+    }
+    generateKnowledgeDoc(projectName, techStack = []) {
+        const stackLine = techStack.length > 0
+            ? `\n## Tech Stack\n${techStack.map((t) => `- ${t}`).join('\n')}\n`
+            : '';
+        return `# ${projectName}
+${stackLine}
+## SCALE Engine Integration (Aider)
+
+This project uses SCALE Engine for AI engineering governance via Aider CLI.
+
+### Commands
+- \`scale create <type> <title>\` — Create artifact
+- \`scale transition <id> <action>\` — Transition artifact state
+- \`scale list --type Spec\` — List artifacts
+- \`scale role activate <role>\` — Switch role
+- \`scale doctor\` — Health check
+
+### Workflow
+1. **Explore** → Role: explorer (Read/Grep only)
+2. **Plan** → Create Spec → refine → approve (guard: ambiguity ≤ 0.2)
+3. **Implement** → Role: implementer (Edit/Write/Bash unlocked)
+4. **Verify** → Must run tests before claiming done
+5. **Learn** → Defects → Lessons → Rules → Hooks
+
+### Rules
+- 🔴 Dangerous commands are physically blocked
+- 🔴 Hardcoded secrets are blocked on Edit/Write
+- 🟡 3 identical retries triggers brute-retry detection
+- 🟡 Claiming done without running tests is blocked
+- 🟢 All tool calls are tracked in .scale/events/
+
+### Aider-Specific Notes
+- Aider uses \`/add\` and \`/drop\` to manage context files
+- Use \`/run\` for shell commands (SCALE hooks apply)
+- Use \`/clear\` to reset context between phases
+- SCALE hooks are defined in \`.aider.conf.yml\`
+
+### Quick Reference
+\`\`\`
+# Start with exploration
+> /add src/
+> /read AIDER.md
+
+# Plan phase
+> scale create Spec "Feature name"
+
+# Implement
+> scale role activate implementer
+> (make changes)
+
+# Verify
+> /run npm test
+
+# Complete
+> scale transition <id> approve
+\`\`\`
+`;
+    }
+    async init(config) {
+        this.projectDir = config.projectDir;
+        this.scaleDir = config.scaleDir ?? join(config.projectDir, '.scale');
+        const created = [];
+        const skipped = [];
+        // Create .scale subdirectories
+        for (const dir of ['events', 'artifacts', 'rules', 'hooks', 'checkpoints']) {
+            const fullDir = join(this.scaleDir, dir);
+            if (!existsSync(fullDir)) {
+                mkdirSync(fullDir, { recursive: true });
+                created.push(fullDir);
+            }
+            else {
+                skipped.push(fullDir);
+            }
+        }
+        // Create .aider directory for commands
+        const aiderDir = join(this.projectDir, '.aider', 'commands');
+        if (!existsSync(aiderDir)) {
+            mkdirSync(aiderDir, { recursive: true });
+            created.push(aiderDir);
+        }
+        else {
+            skipped.push(aiderDir);
+        }
+        // Create/merge .aider.conf.yml
+        const settingsPath = this.getSettingsPath();
+        if (existsSync(settingsPath)) {
+            // Parse existing YAML (simple approach: check for SCALE hooks)
+            const existingYaml = readFileSync(settingsPath, 'utf-8');
+            if (existingYaml.includes('scale gate')) {
+                skipped.push(settingsPath + ' (already integrated)');
+            }
+            else {
+                // Merge: prepend SCALE hooks
+                const generated = this.generateSettings();
+                const yamlContent = this.settingsToYaml(generated);
+                // Insert after header comments
+                const existingLines = existingYaml.split('\n');
+                let insertIndex = 0;
+                for (let i = 0; i < existingLines.length; i++) {
+                    if (existingLines[i].startsWith('#') || existingLines[i].trim() === '') {
+                        insertIndex = i + 1;
+                    }
+                    else {
+                        break;
+                    }
+                }
+                const merged = existingLines.slice(0, insertIndex).join('\n') + '\n' + yamlContent + '\n' + existingLines.slice(insertIndex).join('\n');
+                writeFileSync(settingsPath, merged.trimStart(), 'utf-8');
+                skipped.push(settingsPath + ' (merged)');
+            }
+        }
+        else {
+            const generated = this.generateSettings();
+            const yamlContent = this.settingsToYaml(generated);
+            writeFileSync(settingsPath, yamlContent, 'utf-8');
+            created.push(settingsPath);
+        }
+        // Create AIDER.md knowledge doc
+        const knowledgeDocPath = this.getKnowledgeDocPath();
+        if (!existsSync(knowledgeDocPath)) {
+            const projectName = config.projectDir.split(/[/\\]/).pop() ?? 'Project';
+            writeFileSync(knowledgeDocPath, this.generateKnowledgeDoc(projectName), 'utf-8');
+            created.push(knowledgeDocPath);
+        }
+        else {
+            skipped.push(knowledgeDocPath);
+        }
+        // Create .scale/.gitignore
+        const gitignorePath = join(this.scaleDir, '.gitignore');
+        if (!existsSync(gitignorePath)) {
+            writeFileSync(gitignorePath, `*.db\n*.db-journal\nevents/\ncheckpoints/\nevidence/\nstate/\nhooks/*.sh\n`, 'utf-8');
+            created.push(gitignorePath);
+        }
+        logger.info({ created: created.length, skipped: skipped.length }, 'SCALE init (aider) completed');
+        return {
+            settingsPath,
+            knowledgeDocPath,
+            scaleDir: this.scaleDir,
+            created,
+            skipped,
+        };
+    }
+}
+//# sourceMappingURL=AiderAdapter.js.map

package/dist/adapters/AiderAdapter.js.map

@@ -0,0 +1 @@
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package/dist/adapters/AntigravityAdapter.d.ts

@@ -0,0 +1,4 @@
+import { GenericProjectAgentAdapter } from './GenericProjectAgentAdapter.js';
+export declare class AntigravityAdapter extends GenericProjectAgentAdapter {
+    constructor();
+}