diff --git a/README.md b/README.md
new file mode 100644
index 0000000..1f7ad92
--- /dev/null
+++ b/README.md
@@ -0,0 +1,59 @@
+# Video-Tree-TRM5
+
+> 在层次化视频树上构建可自我进化的搜索 Agent 与可训练递归检索器，实现长视频理解。目标会议：EMNLP 2026。
+
+## 系统概览
+
+本项目是 Video-Tree-TRM4（MVP）的生产级重构，采用 Clean Architecture 分层设计。
+
+### 核心思想：自进化循环对标 PyTorch 训练
+
+| PyTorch | 本项目 | 模块 |
+|---------|--------|------|
+| DataLoader | 出题 question_gen | `app/question_gen/` |
+| model.forward() | 推理 inference | `app/harness/inference.py` + `core/agent/loop.py` |
+| loss.backward() | 诊断 diagnose | `core/evolution/diagnose.py` |
+| optimizer.step() | 进化 evolve | `core/evolution/evolve.py` |
+| nn.Parameter | Skills + Prompts（版本化） | `store/skills/`, `store/prompts/` |
+
+### 三大模块
+
+| 模块 | 目录 | 说明 |
+|------|------|------|
+| 建树 | `app/tree/` | 离线预处理：VLM 生成三层 TreeIndex（L1段落→L2片段→L3帧），支持字幕注入和后增强 |
+| 训练 | `app/harness/` + `core/` | 自进化循环：推理→诊断→进化，含 CE-Gate 统计检验、信息阶梯、mini-batch 调度 |
+| 新题构建 | `app/question_gen/` | 生成 Video-MME 风格训练题，原始 benchmark 作 held-out 泛化评测 |
+
+### 可提取内核
+
+`core/agent/` 和 `core/evolution/` 只依赖 Protocol 接口，可独立提取用于其他项目。
+
+## 快速开始
+
+```bash
+# 1. 创建 Conda 环境
+conda create -n Video-Tree-TRM python=3.11 -y
+conda activate Video-Tree-TRM
+pip install -e ".[dev]"
+
+# 2. 配置环境变量
+cp .env.example .env
+# 编辑 .env 填入 API 密钥
+
+# 3. 验证
+make lint
+make test
+```
+
+## 项目结构
+
+详见 `research-wiki/ARCHITECTURE.md`。
+
+## 文档
+
+| 文档 | 说明 |
+|------|------|
+| `research-wiki/ARCHITECTURE.md` | 系统架构与边界 |
+| `research-wiki/overview.md` | 自进化循环总览 |
+| `CLAUDE.md` | Agent 工作指令 |
+| `reference/docs/architecture.md` | 建树+检索器参考设计 |
diff --git a/adapters/__init__.py b/adapters/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/app/__init__.py b/app/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/app/harness/__init__.py b/app/harness/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/app/ports.py b/app/ports.py
new file mode 100644
index 0000000..ed6ba2e
--- /dev/null
+++ b/app/ports.py
@@ -0,0 +1 @@
+"""应用层 Protocol 端口定义。"""
diff --git a/app/question_gen/__init__.py b/app/question_gen/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/app/retriever/__init__.py b/app/retriever/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/app/search/__init__.py b/app/search/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/app/tree/__init__.py b/app/tree/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/app/tree/enhance/__init__.py b/app/tree/enhance/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/core/__init__.py b/core/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/core/agent/__init__.py b/core/agent/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/core/evolution/__init__.py b/core/evolution/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/core/types.py b/core/types.py
new file mode 100644
index 0000000..28ca3cb
--- /dev/null
+++ b/core/types.py
@@ -0,0 +1 @@
+"""跨模块共享类型。"""
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..643ee1b
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,59 @@
+[build-system]
+requires = ["setuptools>=68.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "video-tree-trm"
+version = "0.1.0"
+description = "自进化搜索 Agent + 可训练递归检索器，在层次化视频树上实现长视频理解"
+requires-python = ">=3.11"
+dependencies = [
+    "torch>=2.1",
+    "pluggy>=1.3",
+    "loguru>=0.7",
+    "openai>=1.30",
+    "httpx>=0.27",
+    "sentence-transformers>=3.0",
+    "numpy>=1.26",
+    "pydantic>=2.5",
+    "pydantic-settings>=2.1",
+    "pyyaml>=6.0",
+    "python-dotenv>=1.0",
+    "opencv-python-headless>=4.9",
+    "json-repair>=0.28",
+    "arq>=0.26",
+    "redis>=5.0",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=8.0",
+    "pytest-cov>=5.0",
+    "pytest-asyncio>=0.23",
+    "ruff>=0.5",
+    "radon>=6.0",
+]
+
+[tool.setuptools.packages.find]
+include = ["core*", "app*", "adapters*"]
+
+[tool.pytest.ini_options]
+pythonpath = [".", ".claude/tools"]
+testpaths = ["tests"]
+markers = [
+    "requires_redis: 需要可达的 Redis（无则 skip）",
+    "requires_gpu: 需要 GPU（无则 skip）",
+    "slow: 慢速测试（CI 按需跑）",
+]
+asyncio_mode = "auto"
+
+[tool.ruff]
+target-version = "py311"
+line-length = 100
+
+[tool.ruff.lint]
+select = ["E", "F", "W", "I", "N", "UP", "B", "A", "C4", "SIM", "TCH"]
+ignore = ["E501"]
+
+[tool.ruff.lint.isort]
+known-first-party = ["core", "app", "adapters"]
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/e2e/__init__.py b/tests/e2e/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/integration/__init__.py b/tests/integration/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/unit/__init__.py b/tests/unit/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/unit/test_smoke.py b/tests/unit/test_smoke.py
new file mode 100644
index 0000000..b16e7c2
--- /dev/null
+++ b/tests/unit/test_smoke.py
@@ -0,0 +1,19 @@
+"""冒烟测试：验证包可导入。"""
+
+
+def test_core_importable():
+    """core 包可导入。"""
+    import core
+    assert core is not None
+
+
+def test_app_importable():
+    """app 包可导入。"""
+    import app
+    assert app is not None
+
+
+def test_adapters_importable():
+    """adapters 包可导入。"""
+    import adapters
+    assert adapters is not None