ai-enderun 0.0.6 → 0.0.7

package/.enderun/PROJECT_MEMORY.md

@@ -15,7 +15,7 @@ This file is the Single Source of Truth (SSOT) and the persistent memory of the
 | Project Name | AI-Enderun |
 | Platform | Agent skill sandbox / orchestration framework |
 | Frontend | React 19 + Vite + Zustand + Panda CSS |
-| Backend | Node.js 20+ + Fastify |
+| Backend | Node.js 20+ + Fastify + Kysely |
 | DB | PostgreSQL |
 | Auth | Not yet defined |
 | Deploy | Not yet defined |
@@ -57,11 +57,74 @@ This file is the Single Source of Truth (SSOT) and the persistent memory of the
 | Trace ID | Task | Agent | Priority | Status |
 | :--- | :--- | :--- | :--- | :--- |
 | 01KR44729Z08BQQ4FCDAVNC148 | Documentation Overhaul & Agent Evangelism | @manager | P1 | COMPLETED |
+| 01KR45N4S0XW6F7G6T1W8F9D2V | Smart Init System Implementation | @manager | P1 | COMPLETED |
+| 01KR45Q8N1V7Z7H9R2M3W9X4Y1 | Robust Access Law & Tool Failure Resolution | @manager | P1 | COMPLETED |
+| 01KR45W2Z91Y5K8M2T3V4X9N7R | Documentation Path Alignment (Root docs/ Fix) | @manager | P1 | COMPLETED |
+| 01KR45Y0M2X3V1B7D9N4Z2K8L5 | README Quick Start Guide Addition | @manager | P2 | COMPLETED |
+| 01KR460M3N1B5V9X2D4Z8L7K1R | Tech-Stack.md Relocation (Root docs/ Fix) | @manager | P1 | COMPLETED |
+| 01KR463F8N1V7W2Z9M3D4G7H5K | Version Bump to v0.0.7 & Health Check | @manager | P1 | COMPLETED |
+| 01KR4666M2X9R1T4V8D7Z2L5K1 | @manager SOP Hardening (MCP Health Check) | @manager | P1 | COMPLETED |
 | 01KR444BM94P5W3ERVJ3YJ9T01 | Agent Report Version Synchronization (v0.0.6) | @manager | P1 | COMPLETED |
 | 01KR442W6MP3GXHF7TD32GJG1V | Agent SOP Hardening & Continuity Alignment | @manager | P1 | COMPLETED |
 
 ## HISTORY (Persistent Memory)
 
+### 2026-05-08 — @manager SOP Hardening (MCP Health Check)
+
+- **Agent:** @manager
+- **Trace ID:** 01KR4666M2X9R1T4V8D7Z2L5K1
+- **Action:** Hardened the `@manager` SOP by adding a mandatory MCP health check to the startup protocol. The manager must now verify connectivity at the beginning of every session and warn the user if tools are unresponsive.
+- **Decision:** Shifted some health monitoring responsibility to the agent level to ensure the orchestration environment is always valid during active sessions.
+- **Next Step:** Observe agent behavior during startup and verify they correctly report MCP issues.
+
+### 2026-05-08 — Version Bump to v0.0.7 & Health Check
+
+- **Agent:** @manager
+- **Trace ID:** 01KR463F8N1V7W2Z9M3D4G7H5K
+- **Action:** Bumped framework version to `v0.0.7`. Implemented `ai-enderun check` command to verify framework health, directory existence, and MCP server readiness. Added automated warnings for missing dependencies and builds during `init`.
+- **Decision:** Prioritized user experience by providing a verification tool to ensure the complex multi-component framework is correctly set up before starting orchestration.
+- **Next Step:** Encourage users to run `ai-enderun check` as part of their initial setup.
+
+### 2026-05-08 — Tech-Stack.md Relocation (Root docs/ Fix)
+
+- **Agent:** @manager
+- **Trace ID:** 01KR460M3N1B5V9X2D4Z8L7K1R
+- **Action:** Relocated `tech-stack.md` from `.enderun/docs/` to the root `docs/` directory. Updated `ENDERUN.md`, `README.md`, Agent SOPs, and MCP gap detection logic to reflect this change.
+- **Decision:** Centralized all project-specific "What" and "How" documentation in the root `docs/` folder to improve visibility and clarify the separation between project requirements and framework internals.
+- **Next Step:** Verify that agents are correctly auditing both requirements and tech stack from the root `docs/` folder.
+
+### 2026-05-08 — README Quick Start Guide Addition
+
+- **Agent:** @manager
+- **Trace ID:** 01KR45Y0M2X3V1B7D9N4Z2K8L5
+- **Action:** Added a bilingual "Getting Started / Başlangıç Rehberi" section to the root `README.md`. Outlined the 5 critical steps for users to take after framework initialization to begin their orchestration journey.
+- **Decision:** Improved user onboarding by providing clear, actionable post-install instructions directly in the main project entry point.
+- **Next Step:** Maintain documentation clarity as new features are added.
+
+### 2026-05-08 — Documentation Path Alignment (Root docs/ Fix)
+
+- **Agent:** @manager
+- **Trace ID:** 01KR45W2Z91Y5K8M2T3V4X9N7R
+- **Action:** Corrected outdated path references in `ENDERUN.md` and `framework-mcp`. Ensured that agents look for project requirements in root `docs/` and technical API contracts in `.enderun/docs/api`.
+- **Decision:** Fully aligned all framework logic with the decoupled documentation model to eliminate agent confusion.
+- **Next Step:** Verify that agents are now correctly identifying project requirements in the root `docs/` folder.
+
+### 2026-05-08 — Robust Access Law & Tool Failure Resolution
+
+- **Agent:** @manager
+- **Trace ID:** 01KR45Q8N1V7Z7H9R2M3W9X4Y1
+- **Action:** Resolved agent failures regarding `Shell date` and direct `ReadFile` of `.enderun/PROJECT_MEMORY.md`. Implemented `get_system_time` and `read_project_memory` MCP tools. Established the "Robust Access Law" in `ENDERUN.md` and updated all Agent SOPs to mandate these tools.
+- **Decision:** Mandated MCP tools for sensitive operations to bypass shell environment inconsistencies and restricted file access in certain agent environments.
+- **Next Step:** Monitor agent stability and ensure all clients correctly utilize the new tools.
+
+### 2026-05-08 — Smart Init System Implementation
+
+- **Agent:** @manager
+- **Trace ID:** 01KR45N4S0XW6F7G6T1W8F9D2V
+- **Action:** Upgraded the `ai-enderun init` command to a "Smart Init" system. Refactored `bin/cli.js` to support `package.json` merging, `.gitignore` updates, and automated `PROJECT_MEMORY.md` initialization. Excluded project-specific state files from the initial framework copy.
+- **Decision:** Shifted from simple file copying to a non-destructive, project-aware initialization process to improve user experience and framework adoption.
+- **Next Step:** Monitor user feedback and refine adapter-specific smart setup logic.
+
 ### 2026-05-08 — Documentation Overhaul & Agent Evangelism
 
 - **Agent:** @manager

package/.enderun/agents/analyst.md

@@ -3,7 +3,7 @@ name: analyst
 description: "Project memory, QA gate, and documentation specialist. Reads PROJECT_MEMORY in every session, audits phase transitions, generates walkthroughs, and writes logs."
 ---
 
-# Project Analyst & QA Gate — v0.0.6 Master
+# Project Analyst & QA Gate — v0.0.7 Master
 
 **Role:** Maintain project memory, serve as a quality gate, and manage documentation. The following protocols are automatically applied in every task.
 
@@ -17,7 +17,7 @@ When analyzing or preparing documentation, never read the content of a file just
 
 ## 🧠 Memory Management (Mandatory in Every Session)
 
-`.enderun/PROJECT_MEMORY.md` is read at the beginning of every session:
+`.enderun/PROJECT_MEMORY.md` is read at the beginning of every session using the `read_project_memory` tool:
 
 - What is the active phase?
 - What are the latest architectural decisions in `CRITICAL DECISIONS`?
@@ -28,11 +28,11 @@ When analyzing or preparing documentation, never read the content of a file just
 ### Writing — Lock Protocol
 
 ```
-1. Is .enderun/PROJECT_MEMORY.lock present?
+1. Is .enderun/PROJECT_MEMORY.lock present? (Check via list_dir or file check)
    └─ If yes: Wait 1s, retry (max 5 attempts)
    └─ After 5 attempts: Report "BLOCKED — Memory Lock Timeout"
 2. Create lock
-3. Write to PROJECT_MEMORY.md (Prefer using update_project_memory tool)
+3. Write to PROJECT_MEMORY.md (MUST use update_project_memory tool)
 4. Delete lock
 ```
 
@@ -169,7 +169,7 @@ Use the `log_agent_action` tool to record your activities securely.
 
 ---
 
-**Agent Completion Report** (v0.0.6)
+**Agent Completion Report** (v0.0.7)
 
 - Mock used? [ ] No / [ ] Yes
 - shared-types changed? [ ] No / [ ] Yes

package/.enderun/agents/backend.md

@@ -3,7 +3,7 @@ name: backend
 description: "Backend Architect. Expert in Node.js, Fastify, Kysely, and PostgreSQL. Leader of Contract and Database. Automatically applies backend-architecture standards in every task."
 ---
 
-# Backend Architect — v0.0.6 Master
+# Backend Architect — v0.0.7 Master
 
 **Role:** Build a secure, high-performance, and consistent server architecture. All the following standards are automatically applied in every task — no need for the user to specify them separately.
 
@@ -219,7 +219,7 @@ When `shared-types` changes:
 
 ---
 
-**Agent Completion Report** (v0.0.6)
+**Agent Completion Report** (v0.0.7)
 - Mock used? [ ] No / [ ] Yes
 - shared-types changed? [ ] No / [ ] Yes → contract.version updated
 - **API contract written? [ ] No / [ ] Yes → .enderun/docs/api/[domain].md**

package/.enderun/agents/explorer.md

@@ -3,7 +3,7 @@ name: explorer
 description: "Codebase Research & Dependency Specialist. Expert in analyzing complex codebases, identifying architectural gaps, and suggesting improvements. Automatically provides context in every research task."
 ---
 
-# Codebase Explorer — v0.0.6 Master
+# Codebase Explorer — v0.0.7 Master
 
 **Role:** Analyze the codebase, map architectures, and understand system-wide dependencies. Your primary duty is to provide context to other agents.
 
@@ -17,7 +17,7 @@ Never suggest a change without understanding the current state of the codebase.
 
 ## 🔌 SESSION STARTUP PROTOCOL (Mandatory)
 
-1. Read `.enderun/PROJECT_MEMORY.md` → Understand the current state and latest `CRITICAL DECISIONS`.
+1. Read `.enderun/PROJECT_MEMORY.md` via `read_project_memory` tool → Understand the current state and latest `CRITICAL DECISIONS`.
 2. Scan the directory structure → Recognize the core folders (`apps`, `packages`, `.enderun`).
 3. Identify the main configuration files (`package.json`, `tsconfig.json`, `ENDERUN.md`).
 
@@ -79,7 +79,7 @@ Every research report must include:
 
 ---
 
-**Agent Completion Report** (v0.0.6)
+**Agent Completion Report** (v0.0.7)
 
 - Mock used? [ ] No / [ ] Yes
 - Codebase searched? [ ] No / [ ] Yes

package/.enderun/agents/frontend.md

@@ -3,7 +3,7 @@ name: frontend
 description: "UI/UX & Frontend Architect. Expert in React 19, Vite, Zustand, and Panda CSS. Fluid & Modern design specialist. Automatically applies the 'Zero UI Library' and Panda CSS discipline in every task."
 ---
 
-# Frontend Architect — v0.0.6 Master
+# Frontend Architect — v0.0.7 Master
 
 **Role:** Build original, high-performance, and responsive user interfaces. The following protocols are automatically applied in every task — no need for the user to specify them separately.
 
@@ -125,7 +125,7 @@ Frontend never creates its own types for backend data.
 
 ---
 
-**Agent Completion Report** (v0.0.6)
+**Agent Completion Report** (v0.0.7)
 - Mock used? [ ] No / [ ] Yes
 - shared-types imported? [ ] No / [ ] Yes
 - **API contract read? [ ] No / [ ] Yes → .enderun/docs/api/**

package/.enderun/agents/manager.md

@@ -3,7 +3,7 @@ name: manager
 description: "CTO & Controller. Leader who manages project processes, generates Trace IDs, and orchestrates agents via Briefings. Reads ENDERUN.md and PROJECT_MEMORY in every session, validates the phase, and assigns agents."
 ---
 
-# Manager (CTO & Controller) — v0.0.6 Master
+# Manager (CTO & Controller) — v0.0.7 Master
 
 **Role:** Enforce all framework rules without compromise and direct agents to the correct tasks. The following protocols are automatically activated in every session.
 
@@ -20,15 +20,18 @@ description: "CTO & Controller. Leader who manages project processes, generates
 ## 🔌 Session Startup Protocol (Mandatory — Every Session, Cannot Be Skipped)
 
 1. Read `ENDERUN.md` — internalize all rules and the Continuity Principle.
-2. Read `.enderun/PROJECT_MEMORY.md` and extract the following:
+2. Read `.enderun/PROJECT_MEMORY.md` (via `read_project_memory` tool) and extract the following:
    - `CURRENT STATUS` → Which phase are we in? Is there an active Trace ID?
    - `CRITICAL DECISIONS` → What was decided in previous sessions? **MUST COMPLY.**
    - `ACTIVE TASKS` → Are there any ongoing tasks? Has agent assignment been made?
    - `HISTORY` → Read the last 3 entries to understand previous work.
 3. Check `.enderun/docs/api/README.md` → Which endpoints exist? Are there missing contracts?
-4. Check `.enderun/docs/tech-stack.md` — if missing, **STOP and ASK**.
+4. Check root `docs/tech-stack.md` — if missing, **STOP and ASK**.
 5. Check root `docs/` — identify user project requirements/stories.
-6. Identify the current `PHASE` — do not proceed to the next phase without meeting DoD criteria.
+6. **Framework Health Check:** Try to call a simple MCP tool (e.g., `get_framework_status`). 
+   - **If it fails:** Warn the user: "⚠️ MCP Server might be down. Please run `ai-enderun check` to verify."
+   - **If it succeeds:** Proceed normally.
+7. Identify the current `PHASE` — do not proceed to the next phase without meeting DoD criteria.
 
 > ✅ **End of Session Requirement:** Add a summary to `.enderun/PROJECT_MEMORY.md` → `HISTORY` section (via `update_project_memory` tool) and log your actions via `log_agent_action` tool at the end of every response. This step cannot be skipped.
 
@@ -54,7 +57,7 @@ Trace ID: 01H... (26-character ULID)
 
 ---
 
-## Briefing Template v0.0.6 (Mandatory in Every Agent Directive)
+## Briefing Template v0.0.7 (Mandatory in Every Agent Directive)
 
 ```
 ## Agent Directive
@@ -142,7 +145,7 @@ graph TD
 
 ---
 
-**Agent Completion Report** (v0.0.6)
+**Agent Completion Report** (v0.0.7)
 
 - Mock used? [ ] No / [ ] Yes
 - shared-types changed? [ ] No / [ ] Yes

package/.enderun/agents/mobile.md

@@ -3,7 +3,7 @@ name: mobile
 description: "Mobile Application Expert. Specialist in React Native and Expo. Automatically applies mobile-first and high-performance standards in every task."
 ---
 
-# Mobile Architect — v0.0.6 Master
+# Mobile Architect — v0.0.7 Master
 
 **Role:** Build high-performance mobile applications using React Native. Maintain structural and stylistic continuity with the existing mobile codebase. All the following standards are automatically applied in every task.
 
@@ -44,7 +44,7 @@ Never start coding before understanding the current state of the components and
 
 ---
 
-**Agent Completion Report** (v0.0.6)
+**Agent Completion Report** (v0.0.7)
 
 - Mock used? [ ] No / [ ] Yes
 - shared-types imported? [ ] No / [ ] Yes

package/.enderun/agents/native.md

@@ -3,7 +3,7 @@ name: native
 description: "Native Application Expert. Specialist in Rust, Tauri, and Electron. Automatically applies security and performance standards in every task."
 ---
 
-# Native Desktop Architect — v0.0.6 Master
+# Native Desktop Architect — v0.0.7 Master
 
 **Role:** Build secure and efficient desktop applications using Tauri or Electron. Ensure procedural continuity across the native codebase.
 
@@ -43,7 +43,7 @@ Always research the existing codebase and native bridge implementations before a
 
 ---
 
-**Agent Completion Report** (v0.0.6)
+**Agent Completion Report** (v0.0.7)
 
 - Mock used? [ ] No / [ ] Yes
 - shared-types imported? [ ] No / [ ] Yes

package/CLAUDE.md

@@ -1,4 +1,4 @@
-# AI-Enderun — Claude Code Adapter (v0.0.6)
+# AI-Enderun — Claude Code Adapter (v0.0.7)
 
 This file is the Claude Code adapter layer.
 Core framework rules and agent capabilities are defined in `./ENDERUN.md`.

package/CODEX.md

@@ -1,4 +1,4 @@
-# AI-Enderun — Codex Adapter (v0.0.6)
+# AI-Enderun — Codex Adapter (v0.0.7)
 
 This file is the Codex adapter layer.
 Core framework rules and agent capabilities are defined in `./ENDERUN.md`.

package/CURSOR.md

@@ -1,4 +1,4 @@
-# AI-Enderun — Cursor Adapter (v0.0.6)
+# AI-Enderun — Cursor Adapter (v0.0.7)
 
 This file is the Cursor adapter layer.
 Core framework rules and agent capabilities are defined in `./ENDERUN.md`.

package/ENDERUN.md

@@ -1,4 +1,4 @@
-# AI-Enderun — Supreme Performance AI Orchestration (v0.0.6)
+# AI-Enderun — Supreme Performance AI Orchestration (v0.0.7)
 
 # Place in project root. This file is the single source of truth for all AI clients (Gemini CLI, Claude Code, etc.).
 
@@ -34,7 +34,7 @@ This project is an "Agent Development School" designed to maximize the professio
    - `PROJECT DEFINITION` and `DOD STATUS` sections → Is the architectural framework and phase quality clear?
    - `HISTORY` section → Read the last 3 entries to understand previous work.
 
-3. **Check `.enderun/docs/` Folder:** Verify if `tech-stack.md` and `project-docs.md` exist.
+3. **Check Documentation:** Verify if root `docs/tech-stack.md` and root `docs/project-docs.md` exist.
 
 4. **Default Stack:**
    - **Frontend:** React 19 + Vite (SPA) + Zustand + Panda CSS.
@@ -121,6 +121,7 @@ Trace ID: 01H... (26-character ULID)
   - **Exception 2:** Unit Tests → Mocks allowed for external dependencies.
 - **Branded Types Law:** All IDs must be Branded Types (`packages/shared-types`).
 - **Search Before Reading:** No agent should read a file blindly; first scan the context with `search_codebase`, `analyze_dependencies`, `get_memory_insights`, and `get_project_gaps`. Legacy prompt compatibility aliases like `codebase_search`, `codebase_graph_query`, `codebase_context`, `codebase_context_search`, and `codebase_status` are also supported.
+- **Robust Access Law:** Agents MUST use MCP tools for system time (`get_system_time`) and memory reading (`read_project_memory`). Using Shell `date` or direct `ReadFile` on `.enderun/PROJECT_MEMORY.md` is strictly forbidden to ensure cross-platform stability.
 - **Procedural Continuity:** Agents MUST maintain consistency with existing code patterns. Before editing any file, analyze its current style, library usage, and architectural approach. Finish a task using the same standards it was started with. If a pattern change is required, it must be approved by @manager and recorded in `CRITICAL DECISIONS`.
 - **Full-Spectrum Responsive:** Every component starts mobile-first (320px) and must remain fluid using `clamp()` and `aspect-ratio` up to ultra-wide screens (1920px+).
 - **Supreme Frontend Aesthetics:** @frontend must avoid "AI slop" aesthetics; design original, characterful, and production-quality interfaces. **Zero UI Library Policy:** Agents never use ready-made component libraries like `shadcn/ui`, `MUI`, or `Chakra UI`. All UI components (Button, Modal, Input, etc.) must be built from scratch using Panda CSS, unique to the project.
@@ -288,7 +289,7 @@ _Logs are stored as a **JSON Array**. Every turn appends a new object to the arr
 
 ---
 
-**Agent Completion Report** (v1.0.6)
+**Agent Completion Report** (v1.0.7)
 
 - Mock used? [ ] No / [ ] Yes
 - shared-types changed? [ ] No / [ ] Yes

package/GEMINI.md

@@ -1,4 +1,4 @@
-# AI-Enderun — General Agent Adapter (v0.0.6)
+# AI-Enderun — General Agent Adapter (v0.0.7)
 
 This file is the general adapter layer for AI agents (Gemini, GPT-4o, etc.).
 Core framework rules and agent capabilities are defined in `./ENDERUN.md`.

package/README.md

@@ -1,4 +1,4 @@
-# AI-Enderun v0.0.6
+# AI-Enderun v0.0.7
 
 English | [Turkce](#turkce)
 
@@ -19,6 +19,14 @@ AI-Enderun provides a structured operating model for AI-driven software delivery
 - `packages/framework-mcp` exposes the MCP server and framework tools.
 - `bin/cli.js` provides the `ai-enderun` CLI.
 
+### 🚀 Getting Started
+
+1.  **Initialize:** Run `npx ai-enderun init gemini` (or `claude`, `cursor`, `codex`).
+2.  **Define Stack:** Fill in your project's technology stack in `docs/tech-stack.md`.
+3.  **Define Requirements:** Place your project goals and user stories in the root `docs/project-docs.md` file.
+4.  **Start Orchestration:** Generate your first Trace ID (ULID): `ai-enderun trace:new "Initial project setup"`
+5.  **Collaborate:** Talk to your AI assistant. It will automatically detect the `ENDERUN.md` constitution and follow the specialized SOPs in `.enderun/agents/`.
+
 ### Directory Model
 
 ```text
@@ -26,14 +34,14 @@ AI-Enderun provides a structured operating model for AI-driven software delivery
 |-- .enderun/
 |   |-- agents/             # Agent SOP (Standard Operating Procedure) files
 |   |-- docs/               # Framework-specific technical documentation
-|   |   |-- tech-stack.md
 |   |   |-- ARCHITECTURE.md
 |   |   `-- api/            # API Contracts (OpenAPI/Shared-types)
 |   |-- logs/               # Structured JSON logs of agent actions
 |   |-- PROJECT_MEMORY.md   # Single Source of Truth for project state
 |   `-- config.json
 |-- docs/                   # User project requirements (The "What" to build)
-|   `-- project-docs.md
+|   |-- project-docs.md
+|   `-- tech-stack.md
 |-- packages/
 |   |-- framework-mcp/      # Core MCP server tools
 |   `-- shared-types/       # Contract-first type definitions
@@ -108,7 +116,15 @@ ai-enderun trace:new <desc>  # Yeni bir gorev zinciri (ULID) baslatir
 ai-enderun verify-contract   # Kontrat uyumunu kontrol eder
 ```
 
-### v0.0.6 Yenilikleri
+### 🚀 Başlangıç Rehberi
+
+1.  **Kurulum:** `npx ai-enderun init gemini` (veya `claude`, `cursor`, `codex`) komutunu çalıştırın.
+2.  **Teknoloji Yığınını Belirleyin:** `docs/tech-stack.md` dosyasını projenize göre doldurun.
+3.  **Gereksinimleri Ekleyin:** Proje hedeflerinizi ve kullanıcı hikayelerinizi kök dizindeki `docs/project-docs.md` dosyasına yerleştirin.
+4.  **Görevi Başlatın:** İlk görev zincirini (ULID) oluşturun: `ai-enderun trace:new "Proje iskeletini oluştur"`
+5.  **Ajanlarla Çalışın:** Yapay zeka yardımcınızla konuşun. Artık projenizdeki `ENDERUN.md` anayasasını ve `.enderun/agents/` içindeki uzman rollerini tanıyarak disiplinli bir şekilde çalışacaktır.
+
+### v0.0.7 Yenilikleri
 
 - **Akilli Kurulum:** Gemini icin otomatik symlink, Claude icin otomatik MCP kurulum yardimcisi.
 - **Süreklilik İlkesi:** Ajanlarin mevcut kod yazim tarzina ve mimari kararlara sadik kalma zorunlulugu.

package/bin/cli.js

@@ -10,6 +10,9 @@ const __dirname = path.dirname(__filename);
 const sourceDir = path.join(__dirname, "..");
 const targetDir = process.cwd();
 
+// --- CONSTANTS ---
+const FRAMEWORK_VERSION = "0.0.7";
+
 // --- HELPER FUNCTIONS ---
 
 function getPackageVersion() {
@@ -89,6 +92,138 @@ function normalizePriority(priority) {
   return /^P[0-3]$/.test(normalized) ? normalized : "P2";
 }
 
+function mergePackageJson(targetPath, sourcePath) {
+  let targetPkg = {};
+  if (fs.existsSync(targetPath)) {
+    try {
+      targetPkg = JSON.parse(fs.readFileSync(targetPath, "utf8"));
+    } catch (e) {
+      console.warn("⚠️  Could not parse existing package.json, creating a new one.");
+    }
+  }
+
+  const sourcePkg = JSON.parse(fs.readFileSync(sourcePath, "utf8"));
+
+  // Merge scripts
+  targetPkg.scripts = {
+    ...targetPkg.scripts,
+    "enderun:status": "ai-enderun status",
+    "enderun:trace": "ai-enderun trace:new",
+    "enderun:verify": "ai-enderun verify-contract",
+  };
+
+  // Ensure basic fields
+  if (!targetPkg.name) targetPkg.name = path.basename(process.cwd());
+  if (!targetPkg.version) targetPkg.version = "0.1.0";
+  if (!targetPkg.type) targetPkg.type = "module";
+
+  // Add metadata
+  targetPkg.enderun = {
+    version: sourcePkg.version,
+    initializedAt: new Date().toISOString(),
+  };
+
+  fs.writeFileSync(targetPath, JSON.stringify(targetPkg, null, 2));
+  console.log("✅ package.json updated with Enderun scripts.");
+}
+
+function updateGitIgnore(targetPath) {
+  const IGNORE_LINES = [
+    ".enderun/*.lock",
+    ".enderun/logs/*.json",
+    "node_modules",
+    ".DS_Store",
+    ".env",
+  ];
+
+  let content = "";
+  if (fs.existsSync(targetPath)) {
+    content = fs.readFileSync(targetPath, "utf8");
+  }
+
+  const lines = content.split("\n").map((l) => l.trim());
+  let added = false;
+
+  for (const line of IGNORE_LINES) {
+    if (!lines.includes(line)) {
+      content += (content.endsWith("\n") || content === "" ? "" : "\n") + line + "\n";
+      added = true;
+    }
+  }
+
+  if (added) {
+    fs.writeFileSync(targetPath, content);
+    console.log("✅ .gitignore updated.");
+  }
+}
+
+function initializeMemory(memoryPath) {
+  if (fs.existsSync(memoryPath)) return;
+
+  const traceId = generateULID();
+  const date = new Date().toISOString().split("T")[0];
+  const template = `# PROJECT MEMORY — AI-Enderun
+
+This file is the Single Source of Truth (SSOT) and the persistent memory of the project.
+
+## CURRENT STATUS
+
+| Active Phase | Profile | Last Update | Active Trace ID | Blockers |
+| :----------- | :------ | :---------- | :-------------- | :------- |
+| PHASE_0      | Lightweight | ${date} | ${traceId} | NONE |
+
+## PROJECT DEFINITION
+
+| Field | Value |
+| :--- | :--- |
+| Project Name | ${path.basename(process.cwd())} |
+| Platform | Not defined |
+| Frontend | React 19 + Vite + Panda CSS |
+| Backend | Node.js 20+ + Fastify |
+| DB | PostgreSQL |
+
+## DOD STATUS
+
+| Phase | Status | Note |
+| :--- | :--- | :--- |
+| PHASE_0 | IN_PROGRESS | Initializing project structure |
+| PHASE_1 | PENDING | |
+| PHASE_2 | PENDING | |
+| PHASE_3 | PENDING | |
+| PHASE_4 | PENDING | |
+
+## CRITICAL DECISIONS
+
+| Date | Decision | Rationale | Agent |
+| :--- | :--- | :--- | :--- |
+| ${date} | Project Initialized | Framework setup via CLI | @manager |
+
+## DELIVERABLES
+
+| Module | Status | Agent | Date |
+| :--- | :--- | :--- | :--- |
+
+## ACTIVE TASKS
+
+| Trace ID | Task | Agent | Priority | Status |
+| :--- | :--- | :--- | :--- | :--- |
+| ${traceId} | Framework setup and architecture alignment | @manager | P1 | IN_PROGRESS |
+
+## HISTORY (Persistent Memory)
+
+### ${date} — Framework Initialization
+
+- **Agent:** @manager
+- **Trace ID:** ${traceId}
+- **Action:** Initialized AI-Enderun framework and project structure.
+- **Decision:** Starting with Lightweight profile.
+- **Next Step:** Define user requirements in docs/project-docs.md.
+`;
+
+  fs.writeFileSync(memoryPath, template);
+  console.log("✅ PROJECT_MEMORY.md initialized.");
+}
+
 // --- COMMANDS ---
 
 /**
@@ -108,38 +243,71 @@ async function initCommand(selectedAdapter) {
     "mcp.json",
     "ENDERUN.md",
     "README.md",
-    "package.json",
     "packages/framework-mcp",
     "packages/shared-types",
   ];
 
-  console.log("🚀 Installing AI Agent Framework...");
-  
-  let filesToCopy = [...CORE_FILES];
+  const DIRS_TO_CREATE = [
+    ".enderun/agents",
+    ".enderun/docs/api",
+    ".enderun/logs",
+    "apps/web",
+    "apps/backend",
+    "docs",
+    "packages/shared-types",
+    "packages/framework-mcp",
+  ];
+
+  console.log("🚀 Installing AI-Enderun (Smart Mode)...");
+
+  // Create directories
+  for (const dir of DIRS_TO_CREATE) {
+    const fullPath = path.join(targetDir, dir);
+    if (!fs.existsSync(fullPath)) {
+      fs.mkdirSync(fullPath, { recursive: true });
+      console.log(`📂 Created directory: ${dir}`);
+    }
+  }
+
+  let filesToProcess = [...CORE_FILES];
   
   if (selectedAdapter) {
     if (!ADAPTERS[selectedAdapter]) {
       console.error(`❌ Invalid adapter: ${selectedAdapter}. Available: gemini, claude, cursor, codex`);
       process.exit(1);
     }
-    filesToCopy = [...CORE_FILES, ...ADAPTERS[selectedAdapter]];
+    filesToProcess = [...CORE_FILES, ...ADAPTERS[selectedAdapter]];
   } else {
-    Object.values(ADAPTERS).forEach(list => filesToCopy.push(...list));
+    Object.values(ADAPTERS).forEach(list => filesToProcess.push(...list));
   }
 
-  for (const item of filesToCopy) {
+  for (const item of filesToProcess) {
     const src = path.join(sourceDir, item);
     const dest = path.join(targetDir, item);
     if (fs.existsSync(src)) {
       if (fs.lstatSync(src).isDirectory()) {
-        copyDir(src, dest);
+        // When copying .enderun, skip logs and project-specific state
+        const skipFiles = item === ".enderun" ? ["logs", "PROJECT_MEMORY.md", "BRAIN_DASHBOARD.md", "PROJECT_MEMORY.lock"] : [];
+        copyDir(src, dest, new Set(skipFiles));
       } else {
+        // Special files handling
+        if (item === "package.json") continue;
+        if (item === "ENDERUN.md" && fs.existsSync(dest)) {
+          console.log(`ℹ️  Skipping ENDERUN.md (already exists).`);
+          continue;
+        }
+        
         fs.copyFileSync(src, dest);
       }
-      console.log(`✅ ${item} created.`);
+      console.log(`✅ ${item} processed.`);
     }
   }
 
+  // Smart setup
+  mergePackageJson(path.join(targetDir, "package.json"), path.join(sourceDir, "package.json"));
+  updateGitIgnore(path.join(targetDir, ".gitignore"));
+  initializeMemory(getMemoryPath());
+
   // --- Post-Install Hooks (Smart Setup) ---
   
   console.log("\n🛠️  Running smart configuration for adapters...");
@@ -170,23 +338,83 @@ async function initCommand(selectedAdapter) {
   }
 
   if (selectedAdapter === "cursor" || !selectedAdapter) {
-    // Add cursor-specific rules or settings if needed
-    console.log("✨ Cursor: Adapter CLAUDE.md is ready to guide your AI.");
+    console.log("✨ Cursor: Adapter CLAUDE.md and ENDERUN.md are ready to guide your AI.");
+  }
+
+  console.log("\n✨ Framework successfully installed! (v" + FRAMEWORK_VERSION + ")");
+  console.log("\n⚠️  IMPORTANT: Run 'npm install && npm run build' to prepare the framework.");
+  console.log("👉 Then run 'ai-enderun check' to verify the installation.");
+}
+
+/**
+ * Check framework health and MCP status.
+ */
+function checkCommand() {
+  console.log(`🔍 Checking AI-Enderun Health (v${FRAMEWORK_VERSION})...`);
+  let issues = 0;
+
+  const checks = [
+    { name: "Constitution (ENDERUN.md)", path: "ENDERUN.md" },
+    { name: "Memory (PROJECT_MEMORY.md)", path: ".enderun/PROJECT_MEMORY.md" },
+    { name: "Shared Types", path: "packages/shared-types/package.json" },
+    { name: "MCP Server", path: "packages/framework-mcp/package.json" },
+    { name: "Tech Stack", path: "docs/tech-stack.md" },
+    { name: "Requirements", path: "docs/project-docs.md" },
+  ];
+
+  for (const check of checks) {
+    if (fs.existsSync(path.join(process.cwd(), check.path))) {
+      console.log(`✅ ${check.name} found.`);
+    } else {
+      console.log(`❌ ${check.name} MISSING! (${check.path})`);
+      issues++;
+    }
   }
 
-  console.log("\n✨ Framework successfully installed! (v" + getPackageVersion() + ")");
+  // Dependency Check
+  const mcpNodeModules = path.join(process.cwd(), "packages/framework-mcp/node_modules");
+  if (!fs.existsSync(mcpNodeModules)) {
+    console.log("❌ Dependencies MISSING! (Run 'npm install')");
+    issues++;
+  } else {
+    console.log("✅ Dependencies found.");
+  }
+
+  // MCP Build Check
+  const mcpPath = path.join(process.cwd(), "packages/framework-mcp/dist/index.js");
+  if (!fs.existsSync(mcpPath)) {
+    console.log("❌ MCP Build MISSING! (Run 'npm run build')");
+    issues++;
+  } else {
+    console.log("✅ MCP Build found.");
+    console.log("⏳ Testing MCP Server syntax...");
+    try {
+      execSync(`node --check ${mcpPath}`, { stdio: "pipe" });
+      console.log("✅ MCP Server syntax valid.");
+    } catch (e) {
+      // If --check fails on ESM, we might skip it or use a better check
+      console.log("⚠️  MCP Syntax check skipped (ESM/Environment).");
+    }
+  }
+
+  if (issues === 0) {
+    console.log("\n🚀 All systems green! AI-Enderun is ready for orchestration.");
+  } else {
+    console.log(`\n⚠️  Found ${issues} issues. Please fix them before starting.`);
+  }
 }
 
-function copyDir(src, dest) {
-  const SKIP_NAMES = new Set(["node_modules", ".git", ".DS_Store"]);
+function copyDir(src, dest, skipSet = new Set()) {
+  const DEFAULT_SKIP = new Set(["node_modules", ".git", ".DS_Store"]);
+  const actualSkip = new Set([...DEFAULT_SKIP, ...skipSet]);
 
   fs.mkdirSync(dest, { recursive: true });
   fs.readdirSync(src, { withFileTypes: true }).forEach(entry => {
-    if (SKIP_NAMES.has(entry.name)) return;
+    if (actualSkip.has(entry.name)) return;
 
     const srcPath = path.join(src, entry.name);
     const destPath = path.join(dest, entry.name);
-    entry.isDirectory() ? copyDir(srcPath, destPath) : fs.copyFileSync(srcPath, destPath);
+    entry.isDirectory() ? copyDir(srcPath, destPath, skipSet) : fs.copyFileSync(srcPath, destPath);
   });
 }
 
@@ -319,17 +547,21 @@ async function main() {
     case "verify-contract":
       verifyContractCommand();
       break;
+    case "check":
+      checkCommand();
+      break;
     case "version":
     case "-v":
     case "--version":
-      console.log(`v${getPackageVersion()}`);
+      console.log(`v${FRAMEWORK_VERSION}`);
       break;
     default:
       console.log(`
-🤖 AI-Enderun CLI (v${getPackageVersion()})
+🤖 AI-Enderun CLI (v${FRAMEWORK_VERSION})
 
 Available Commands:
   init [adapter]    Initialize the framework (gemini, claude, cursor, codex)
+  check             Verify framework health and MCP server status
   status            Show current phase and task status
   trace:new <desc>  Generate a new Trace ID and add the task to memory
   verify-contract   Check if shared types match the stored hash

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "ai-enderun",
-  "version": "0.0.6",
+  "version": "0.0.7",
   "description": "Supreme AI Orchestration Framework — Senior Discipline & Ottoman Wisdom",
   "author": "Yusuf BEKAR <ybekar@msn.com>",
   "repository": {

package/packages/framework-mcp/README.md

@@ -1,4 +1,4 @@
-# AI-Enderun MCP Server v0.0.6
+# AI-Enderun MCP Server v0.0.7
 
 English | [Turkce](#turkce)
 

package/packages/framework-mcp/dist/index.js

@@ -8,7 +8,7 @@ import crypto from "crypto";
 import { Project, SyntaxKind } from "ts-morph";
 const server = new Server({
     name: "ai-enderun-mcp",
-    version: "0.0.6",
+    version: "0.0.7",
 }, {
     capabilities: {
         tools: {},
@@ -40,7 +40,7 @@ const LOG_AGENT_ACTION_ARGS_SCHEMA = z.object({
     summary: z.string().min(1),
     details: z.record(z.any()).default({}),
 });
-const FRAMEWORK_VERSION = "0.0.6";
+const FRAMEWORK_VERSION = "0.0.7";
 function resolveSafePath(projectRoot, targetPath) {
     const resolved = path.resolve(projectRoot, targetPath);
     const relative = path.relative(projectRoot, resolved);
@@ -303,6 +303,16 @@ server.setRequestHandler(ListToolsRequestSchema, async () => {
                     required: ["agent", "action", "requestId", "status", "summary"],
                 },
             },
+            {
+                name: "get_system_time",
+                description: "Get the current system time in ISO-8601 format (UTC). Use this instead of Shell 'date' commands.",
+                inputSchema: { type: "object", properties: {} },
+            },
+            {
+                name: "read_project_memory",
+                description: "Read the entire content of .enderun/PROJECT_MEMORY.md safely. Use this instead of direct ReadFile tools to ensure framework compatibility.",
+                inputSchema: { type: "object", properties: {} },
+            },
         ],
     };
 });
@@ -509,11 +519,13 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
             const checkPaths = [
                 { path: "apps", type: "folder", optional: true },
                 { path: "packages/shared-types/src", type: "folder" },
-                { path: "docs/api", type: "folder", optional: true },
+                { path: ".enderun/docs/api", type: "folder", optional: true },
                 { path: ".env", type: "file", optional: true },
                 { path: ".env.example", type: "file" },
                 { path: ".enderun/PROJECT_MEMORY.md", type: "file" },
                 { path: ".enderun/BRAIN_DASHBOARD.md", type: "file" },
+                { path: "docs/tech-stack.md", type: "file" },
+                { path: "docs/project-docs.md", type: "file" },
             ];
             for (const item of checkPaths) {
                 const fullPath = path.join(projectRoot, item.path);
@@ -915,6 +927,24 @@ Contract is invalid or out of date!
                 };
             }
         }
+        case "get_system_time": {
+            return {
+                content: [{ type: "text", text: new Date().toISOString() }],
+            };
+        }
+        case "read_project_memory": {
+            try {
+                const memoryPath = path.join(projectRoot, ".enderun", "PROJECT_MEMORY.md");
+                if (!fs.existsSync(memoryPath)) {
+                    return { content: [{ type: "text", text: "ERROR: PROJECT_MEMORY.md not found." }] };
+                }
+                const content = fs.readFileSync(memoryPath, "utf-8");
+                return { content: [{ type: "text", text: content }] };
+            }
+            catch (error) {
+                return { content: [{ type: "text", text: "ERROR: Failed to read PROJECT_MEMORY.md" }] };
+            }
+        }
         default:
             throw new Error(`Tool not found: ${name}`);
     }

package/packages/framework-mcp/package.json

@@ -1,6 +1,6 @@
 {
   "name": "ai-enderun-mcp",
-  "version": "0.0.6",
+  "version": "0.0.7",
   "description": "Enterprise-grade MCP Server for AI Agent Framework — Memory, Security & AST Intelligence",
   "author": "Yusuf BEKAR <ybekar@msn.com>",
   "repository": {

package/packages/shared-types/README.md

@@ -1,4 +1,4 @@
-# AI-Enderun Shared Types v0.0.6
+# AI-Enderun Shared Types v0.0.7
 
 English | [Turkce](#turkce)
 

package/packages/shared-types/dist/index.d.ts

@@ -1,5 +1,5 @@
 /**
- * Shared Types — AI-Enderun v0.0.6
+ * Shared Types — AI-Enderun v0.0.7
  * Bu paketteki tüm tipler backend ve frontend arasındaki kontratı tanımlar.
  * Sadece @backend düzenler, @frontend okur/import eder.
  */

package/packages/shared-types/dist/index.js

@@ -1,5 +1,5 @@
 /**
- * Shared Types — AI-Enderun v0.0.6
+ * Shared Types — AI-Enderun v0.0.7
  * Bu paketteki tüm tipler backend ve frontend arasındaki kontratı tanımlar.
  * Sadece @backend düzenler, @frontend okur/import eder.
  */

package/packages/shared-types/package.json

@@ -1,6 +1,6 @@
 {
   "name": "ai-enderun-shared-types",
-  "version": "0.0.6",
+  "version": "0.0.7",
   "description": "Shared TypeScript types for AI-Enderun Framework. Ensures Contract-First synchronization between agents.",
   "author": "Yusuf BEKAR <ybekar@msn.com>",
   "repository": {