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+# 🏛️ Repopilot Architecture
+
+Repopilot is an advanced, autonomous AI developer agent capable of independently modifying, testing, and committing code. This document outlines the high-level system architecture, core components, and the execution loop.
+
+---
+
+## 🔄 System Flow Architecture
+
+The architecture relies on an iterative feedback loop, heavily orchestrated by the `AutonomousAgent`. Below is a visualization of the data flow and decision tree inside the system:
+
+```mermaid
+graph TD
+    A([User Input: Task & Repo]) --> B[main.py CLI Parser]
+    B --> C[AgentConfig Initialization]
+    C --> D[AutonomousAgent Orchestrator]
+
+    subgraph AgentLoop["Iterative Execution Loop (Max Iterations)"]
+        D --> E[Repo Ingestion]
+        E --> F[Context Builder]
+        F -->|Prompt Context| G[LLM Client]
+        
+        G -->|Parse Error| G
+        G -->|Low Confidence| H[Skip to Next Iteration]
+        G -->|Code Changes| I[Code Modifier]
+        
+        I -->|Stash & Backup| J[Validate & Apply Changes]
+        J --> K[Sandbox Execution]
+        
+        K -->|Test Success| L{Success Condition}
+        K -->|Test Failure / Timeout| M[Rollback & Feed Error to LLM]
+        M -.-> E
+    end
+
+    L -->|Git Enabled| N[Git Integration]
+    L -->|Git Disabled| O([Complete Task])
+    
+    N --> P[Commit Changes]
+    P --> Q[Push Branch]
+    Q --> R[Create GitHub PR]
+    
+    R --> O
+```
+
+---
+
+## 📦 Core Modules Breakdown
+
+The codebase is highly modular, ensuring each component handles exactly one responsibility. 
+
+### 1. The Orchestrator
+- **`main.py`**: The main CLI entry point. Responsible for parsing arguments (like runner, task, max iterations, Git configuration) and starting the `AutonomousAgent`.
+- **`modules/agent_loop.py`**: Contains the core `AutonomousAgent` class. It manages the `while` loop connecting all other modules, handling logic such as early exits, timeout handling, and Git operations.
+
+### 2. File & Context Management
+- **`modules/repo_ingestion.py`**: Ingests the repository file tree safely, respecting `.gitignore` rules to avoid loading unnecessary files (e.g., node_modules, binaries).
+- **`modules/context_builder.py`**: Controls exactly what text goes to the LLM. It limits the token window to prevent API overflow while ensuring the agent has sufficient context.
+
+### 3. Intelligence & Execution
+- **`modules/llm_client.py`**: The API wrapper for Anthropic. It constructs the system prompts and strictly parses structured JSON responses from the LLM, managing both initial requests and feedback retries.
+- **`modules/code_modifier.py`**: Handles safe file operations. It verifies that target paths belong inside the repo, creates backups, applies literal or diff-based code edits, and provides rollback capabilities if testing fails.
+- **`modules/sandbox.py`**: Executes test commands (`pytest`, `npm test`, etc.) using Python's isolated `subprocess` module. It captures `stdout`, `stderr`, and exit codes while enforcing hard timeouts.
+
+### 4. Version Control Integration
+- **`modules/git_integration.py`**: Wraps local `git` CLI operations (branching, staging, stashing, committing) and interfaces with the GitHub CLI (`gh`) to automatically create Pull Requests and branch tracking.
+
+---
+
+## 🔒 Security & Safety Mechanisms
+
+- **Backup & Rollback:** The `CodeModificationEngine` caches modified files before applying changes. If an iteration completely fails, the original states are restored.
+- **Sandbox Timeouts:** Prevents infinite loops or hanging tests by enforcing strict execution timeouts via `SubprocessSandbox`.
+- **Pre-execution Confidence Check:** Changes with an LLM confidence score below a defined threshold (`min_confidence_to_apply`) are automatically rejected to avoid unstable commits.
+
+---
+
+## 🚀 Future Extensibility
+
+- **Docker Sandbox Integration:** Transitioning from `SubprocessSandbox` to a fully isolated Docker container execution for safer, immutable test runs.
+- **Multi-Model Fallback:** Extending `llm_client.py` to support OpenAI, Gemini, and local models.
+- **AST-based Editing:** Implementing precise AST parsing instead of line-based diffs for modifying code structural integrity safely.