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package/assets/.agent/skills/autonomous-agent-patterns/SKILL.md

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+---
+name: autonomous-agent-patterns
+description: "Design patterns for building autonomous coding agents. Covers tool integration, permission systems, browser automation, and human-in-the-loop workflows. Use when building AI agents, designing tool APIs, implementing permission systems, or creating autonomous coding assistants."
+---
+
+# 🕹️ Autonomous Agent Patterns
+
+> Design patterns for building autonomous coding agents, inspired by [Cline](https://github.com/cline/cline) and [OpenAI Codex](https://github.com/openai/codex).
+
+## When to Use This Skill
+
+Use this skill when:
+
+- Building autonomous AI agents
+- Designing tool/function calling APIs
+- Implementing permission and approval systems
+- Creating browser automation for agents
+- Designing human-in-the-loop workflows
+
+---
+
+## 1. Core Agent Architecture
+
+### 1.1 Agent Loop
+
+```
+┌─────────────────────────────────────────────────────────────┐
+│                     AGENT LOOP                               │
+│                                                              │
+│  ┌──────────┐    ┌──────────┐    ┌──────────┐              │
+│  │  Think   │───▶│  Decide  │───▶│   Act    │              │
+│  │ (Reason) │    │ (Plan)   │    │ (Execute)│              │
+│  └──────────┘    └──────────┘    └──────────┘              │
+│       ▲                               │                     │
+│       │         ┌──────────┐          │                     │
+│       └─────────│ Observe  │◀─────────┘                     │
+│                 │ (Result) │                                │
+│                 └──────────┘                                │
+└─────────────────────────────────────────────────────────────┘
+```
+
+```python
+class AgentLoop:
+    def __init__(self, llm, tools, max_iterations=50):
+        self.llm = llm
+        self.tools = {t.name: t for t in tools}
+        self.max_iterations = max_iterations
+        self.history = []
+
+    def run(self, task: str) -> str:
+        self.history.append({"role": "user", "content": task})
+
+        for i in range(self.max_iterations):
+            # Think: Get LLM response with tool options
+            response = self.llm.chat(
+                messages=self.history,
+                tools=self._format_tools(),
+                tool_choice="auto"
+            )
+
+            # Decide: Check if agent wants to use a tool
+            if response.tool_calls:
+                for tool_call in response.tool_calls:
+                    # Act: Execute the tool
+                    result = self._execute_tool(tool_call)
+
+                    # Observe: Add result to history
+                    self.history.append({
+                        "role": "tool",
+                        "tool_call_id": tool_call.id,
+                        "content": str(result)
+                    })
+            else:
+                # No more tool calls = task complete
+                return response.content
+
+        return "Max iterations reached"
+
+    def _execute_tool(self, tool_call) -> Any:
+        tool = self.tools[tool_call.name]
+        args = json.loads(tool_call.arguments)
+        return tool.execute(**args)
+```
+
+### 1.2 Multi-Model Architecture
+
+```python
+class MultiModelAgent:
+    """
+    Use different models for different purposes:
+    - Fast model for planning
+    - Powerful model for complex reasoning
+    - Specialized model for code generation
+    """
+
+    def __init__(self):
+        self.models = {
+            "fast": "gpt-3.5-turbo",      # Quick decisions
+            "smart": "gpt-4-turbo",        # Complex reasoning
+            "code": "claude-3-sonnet",     # Code generation
+        }
+
+    def select_model(self, task_type: str) -> str:
+        if task_type == "planning":
+            return self.models["fast"]
+        elif task_type == "analysis":
+            return self.models["smart"]
+        elif task_type == "code":
+            return self.models["code"]
+        return self.models["smart"]
+```
+
+---
+
+## 2. Tool Design Patterns
+
+### 2.1 Tool Schema
+
+```python
+class Tool:
+    """Base class for agent tools"""
+
+    @property
+    def schema(self) -> dict:
+        """JSON Schema for the tool"""
+        return {
+            "name": self.name,
+            "description": self.description,
+            "parameters": {
+                "type": "object",
+                "properties": self._get_parameters(),
+                "required": self._get_required()
+            }
+        }
+
+    def execute(self, **kwargs) -> ToolResult:
+        """Execute the tool and return result"""
+        raise NotImplementedError
+
+class ReadFileTool(Tool):
+    name = "read_file"
+    description = "Read the contents of a file from the filesystem"
+
+    def _get_parameters(self):
+        return {
+            "path": {
+                "type": "string",
+                "description": "Absolute path to the file"
+            },
+            "start_line": {
+                "type": "integer",
+                "description": "Line to start reading from (1-indexed)"
+            },
+            "end_line": {
+                "type": "integer",
+                "description": "Line to stop reading at (inclusive)"
+            }
+        }
+
+    def _get_required(self):
+        return ["path"]
+
+    def execute(self, path: str, start_line: int = None, end_line: int = None) -> ToolResult:
+        try:
+            with open(path, 'r') as f:
+                lines = f.readlines()
+
+            if start_line and end_line:
+                lines = lines[start_line-1:end_line]
+
+            return ToolResult(
+                success=True,
+                output="".join(lines)
+            )
+        except FileNotFoundError:
+            return ToolResult(
+                success=False,
+                error=f"File not found: {path}"
+            )
+```
+
+### 2.2 Essential Agent Tools
+
+```python
+CODING_AGENT_TOOLS = {
+    # File operations
+    "read_file": "Read file contents",
+    "write_file": "Create or overwrite a file",
+    "edit_file": "Make targeted edits to a file",
+    "list_directory": "List files and folders",
+    "search_files": "Search for files by pattern",
+
+    # Code understanding
+    "search_code": "Search for code patterns (grep)",
+    "get_definition": "Find function/class definition",
+    "get_references": "Find all references to a symbol",
+
+    # Terminal
+    "run_command": "Execute a shell command",
+    "read_output": "Read command output",
+    "send_input": "Send input to running command",
+
+    # Browser (optional)
+    "open_browser": "Open URL in browser",
+    "click_element": "Click on page element",
+    "type_text": "Type text into input",
+    "screenshot": "Capture screenshot",
+
+    # Context
+    "ask_user": "Ask the user a question",
+    "search_web": "Search the web for information"
+}
+```
+
+### 2.3 Edit Tool Design
+
+```python
+class EditFileTool(Tool):
+    """
+    Precise file editing with conflict detection.
+    Uses search/replace pattern for reliable edits.
+    """
+
+    name = "edit_file"
+    description = "Edit a file by replacing specific content"
+
+    def execute(
+        self,
+        path: str,
+        search: str,
+        replace: str,
+        expected_occurrences: int = 1
+    ) -> ToolResult:
+        """
+        Args:
+            path: File to edit
+            search: Exact text to find (must match exactly, including whitespace)
+            replace: Text to replace with
+            expected_occurrences: How many times search should appear (validation)
+        """
+        with open(path, 'r') as f:
+            content = f.read()
+
+        # Validate
+        actual_occurrences = content.count(search)
+        if actual_occurrences != expected_occurrences:
+            return ToolResult(
+                success=False,
+                error=f"Expected {expected_occurrences} occurrences, found {actual_occurrences}"
+            )
+
+        if actual_occurrences == 0:
+            return ToolResult(
+                success=False,
+                error="Search text not found in file"
+            )
+
+        # Apply edit
+        new_content = content.replace(search, replace)
+
+        with open(path, 'w') as f:
+            f.write(new_content)
+
+        return ToolResult(
+            success=True,
+            output=f"Replaced {actual_occurrences} occurrence(s)"
+        )
+```
+
+---
+
+## 3. Permission & Safety Patterns
+
+### 3.1 Permission Levels
+
+```python
+class PermissionLevel(Enum):
+    # Fully automatic - no user approval needed
+    AUTO = "auto"
+
+    # Ask once per session
+    ASK_ONCE = "ask_once"
+
+    # Ask every time
+    ASK_EACH = "ask_each"
+
+    # Never allow
+    NEVER = "never"
+
+PERMISSION_CONFIG = {
+    # Low risk - can auto-approve
+    "read_file": PermissionLevel.AUTO,
+    "list_directory": PermissionLevel.AUTO,
+    "search_code": PermissionLevel.AUTO,
+
+    # Medium risk - ask once
+    "write_file": PermissionLevel.ASK_ONCE,
+    "edit_file": PermissionLevel.ASK_ONCE,
+
+    # High risk - ask each time
+    "run_command": PermissionLevel.ASK_EACH,
+    "delete_file": PermissionLevel.ASK_EACH,
+
+    # Dangerous - never auto-approve
+    "sudo_command": PermissionLevel.NEVER,
+    "format_disk": PermissionLevel.NEVER
+}
+```
+
+### 3.2 Approval UI Pattern
+
+```python
+class ApprovalManager:
+    def __init__(self, ui, config):
+        self.ui = ui
+        self.config = config
+        self.session_approvals = {}
+
+    def request_approval(self, tool_name: str, args: dict) -> bool:
+        level = self.config.get(tool_name, PermissionLevel.ASK_EACH)
+
+        if level == PermissionLevel.AUTO:
+            return True
+
+        if level == PermissionLevel.NEVER:
+            self.ui.show_error(f"Tool '{tool_name}' is not allowed")
+            return False
+
+        if level == PermissionLevel.ASK_ONCE:
+            if tool_name in self.session_approvals:
+                return self.session_approvals[tool_name]
+
+        # Show approval dialog
+        approved = self.ui.show_approval_dialog(
+            tool=tool_name,
+            args=args,
+            risk_level=self._assess_risk(tool_name, args)
+        )
+
+        if level == PermissionLevel.ASK_ONCE:
+            self.session_approvals[tool_name] = approved
+
+        return approved
+
+    def _assess_risk(self, tool_name: str, args: dict) -> str:
+        """Analyze specific call for risk level"""
+        if tool_name == "run_command":
+            cmd = args.get("command", "")
+            if any(danger in cmd for danger in ["rm -rf", "sudo", "chmod"]):
+                return "HIGH"
+        return "MEDIUM"
+```
+
+### 3.3 Sandboxing
+
+```python
+class SandboxedExecution:
+    """
+    Execute code/commands in isolated environment
+    """
+
+    def __init__(self, workspace_dir: str):
+        self.workspace = workspace_dir
+        self.allowed_commands = ["npm", "python", "node", "git", "ls", "cat"]
+        self.blocked_paths = ["/etc", "/usr", "/bin", os.path.expanduser("~")]
+
+    def validate_path(self, path: str) -> bool:
+        """Ensure path is within workspace"""
+        real_path = os.path.realpath(path)
+        workspace_real = os.path.realpath(self.workspace)
+        return real_path.startswith(workspace_real)
+
+    def validate_command(self, command: str) -> bool:
+        """Check if command is allowed"""
+        cmd_parts = shlex.split(command)
+        if not cmd_parts:
+            return False
+
+        base_cmd = cmd_parts[0]
+        return base_cmd in self.allowed_commands
+
+    def execute_sandboxed(self, command: str) -> ToolResult:
+        if not self.validate_command(command):
+            return ToolResult(
+                success=False,
+                error=f"Command not allowed: {command}"
+            )
+
+        # Execute in isolated environment
+        result = subprocess.run(
+            command,
+            shell=True,
+            cwd=self.workspace,
+            capture_output=True,
+            timeout=30,
+            env={
+                **os.environ,
+                "HOME": self.workspace,  # Isolate home directory
+            }
+        )
+
+        return ToolResult(
+            success=result.returncode == 0,
+            output=result.stdout.decode(),
+            error=result.stderr.decode() if result.returncode != 0 else None
+        )
+```
+
+---
+
+## 4. Browser Automation
+
+### 4.1 Browser Tool Pattern
+
+```python
+class BrowserTool:
+    """
+    Browser automation for agents using Playwright/Puppeteer.
+    Enables visual debugging and web testing.
+    """
+
+    def __init__(self, headless: bool = True):
+        self.browser = None
+        self.page = None
+        self.headless = headless
+
+    async def open_url(self, url: str) -> ToolResult:
+        """Navigate to URL and return page info"""
+        if not self.browser:
+            self.browser = await playwright.chromium.launch(headless=self.headless)
+            self.page = await self.browser.new_page()
+
+        await self.page.goto(url)
+
+        # Capture state
+        screenshot = await self.page.screenshot(type='png')
+        title = await self.page.title()
+
+        return ToolResult(
+            success=True,
+            output=f"Loaded: {title}",
+            metadata={
+                "screenshot": base64.b64encode(screenshot).decode(),
+                "url": self.page.url
+            }
+        )
+
+    async def click(self, selector: str) -> ToolResult:
+        """Click on an element"""
+        try:
+            await self.page.click(selector, timeout=5000)
+            await self.page.wait_for_load_state("networkidle")
+
+            screenshot = await self.page.screenshot()
+            return ToolResult(
+                success=True,
+                output=f"Clicked: {selector}",
+                metadata={"screenshot": base64.b64encode(screenshot).decode()}
+            )
+        except TimeoutError:
+            return ToolResult(
+                success=False,
+                error=f"Element not found: {selector}"
+            )
+
+    async def type_text(self, selector: str, text: str) -> ToolResult:
+        """Type text into an input"""
+        await self.page.fill(selector, text)
+        return ToolResult(success=True, output=f"Typed into {selector}")
+
+    async def get_page_content(self) -> ToolResult:
+        """Get accessible text content of the page"""
+        content = await self.page.evaluate("""
+            () => {
+                // Get visible text
+                const walker = document.createTreeWalker(
+                    document.body,
+                    NodeFilter.SHOW_TEXT,
+                    null,
+                    false
+                );
+
+                let text = '';
+                while (walker.nextNode()) {
+                    const node = walker.currentNode;
+                    if (node.textContent.trim()) {
+                        text += node.textContent.trim() + '\\n';
+                    }
+                }
+                return text;
+            }
+        """)
+        return ToolResult(success=True, output=content)
+```
+
+### 4.2 Visual Agent Pattern
+
+```python
+class VisualAgent:
+    """
+    Agent that uses screenshots to understand web pages.
+    Can identify elements visually without selectors.
+    """
+
+    def __init__(self, llm, browser):
+        self.llm = llm
+        self.browser = browser
+
+    async def describe_page(self) -> str:
+        """Use vision model to describe current page"""
+        screenshot = await self.browser.screenshot()
+
+        response = self.llm.chat([
+            {
+                "role": "user",
+                "content": [
+                    {"type": "text", "text": "Describe this webpage. List all interactive elements you see."},
+                    {"type": "image", "data": screenshot}
+                ]
+            }
+        ])
+
+        return response.content
+
+    async def find_and_click(self, description: str) -> ToolResult:
+        """Find element by visual description and click it"""
+        screenshot = await self.browser.screenshot()
+
+        # Ask vision model to find element
+        response = self.llm.chat([
+            {
+                "role": "user",
+                "content": [
+                    {
+                        "type": "text",
+                        "text": f"""
+                        Find the element matching: "{description}"
+                        Return the approximate coordinates as JSON: {{"x": number, "y": number}}
+                        """
+                    },
+                    {"type": "image", "data": screenshot}
+                ]
+            }
+        ])
+
+        coords = json.loads(response.content)
+        await self.browser.page.mouse.click(coords["x"], coords["y"])
+
+        return ToolResult(success=True, output=f"Clicked at ({coords['x']}, {coords['y']})")
+```
+
+---
+
+## 5. Context Management
+
+### 5.1 Context Injection Patterns
+
+````python
+class ContextManager:
+    """
+    Manage context provided to the agent.
+    Inspired by Cline's @-mention patterns.
+    """
+
+    def __init__(self, workspace: str):
+        self.workspace = workspace
+        self.context = []
+
+    def add_file(self, path: str) -> None:
+        """@file - Add file contents to context"""
+        with open(path, 'r') as f:
+            content = f.read()
+
+        self.context.append({
+            "type": "file",
+            "path": path,
+            "content": content
+        })
+
+    def add_folder(self, path: str, max_files: int = 20) -> None:
+        """@folder - Add all files in folder"""
+        for root, dirs, files in os.walk(path):
+            for file in files[:max_files]:
+                file_path = os.path.join(root, file)
+                self.add_file(file_path)
+
+    def add_url(self, url: str) -> None:
+        """@url - Fetch and add URL content"""
+        response = requests.get(url)
+        content = html_to_markdown(response.text)
+
+        self.context.append({
+            "type": "url",
+            "url": url,
+            "content": content
+        })
+
+    def add_problems(self, diagnostics: list) -> None:
+        """@problems - Add IDE diagnostics"""
+        self.context.append({
+            "type": "diagnostics",
+            "problems": diagnostics
+        })
+
+    def format_for_prompt(self) -> str:
+        """Format all context for LLM prompt"""
+        parts = []
+        for item in self.context:
+            if item["type"] == "file":
+                parts.append(f"## File: {item['path']}\n```\n{item['content']}\n```")
+            elif item["type"] == "url":
+                parts.append(f"## URL: {item['url']}\n{item['content']}")
+            elif item["type"] == "diagnostics":
+                parts.append(f"## Problems:\n{json.dumps(item['problems'], indent=2)}")
+
+        return "\n\n".join(parts)
+````
+
+### 5.2 Checkpoint/Resume
+
+```python
+class CheckpointManager:
+    """
+    Save and restore agent state for long-running tasks.
+    """
+
+    def __init__(self, storage_dir: str):
+        self.storage_dir = storage_dir
+        os.makedirs(storage_dir, exist_ok=True)
+
+    def save_checkpoint(self, session_id: str, state: dict) -> str:
+        """Save current agent state"""
+        checkpoint = {
+            "timestamp": datetime.now().isoformat(),
+            "session_id": session_id,
+            "history": state["history"],
+            "context": state["context"],
+            "workspace_state": self._capture_workspace(state["workspace"]),
+            "metadata": state.get("metadata", {})
+        }
+
+        path = os.path.join(self.storage_dir, f"{session_id}.json")
+        with open(path, 'w') as f:
+            json.dump(checkpoint, f, indent=2)
+
+        return path
+
+    def restore_checkpoint(self, checkpoint_path: str) -> dict:
+        """Restore agent state from checkpoint"""
+        with open(checkpoint_path, 'r') as f:
+            checkpoint = json.load(f)
+
+        return {
+            "history": checkpoint["history"],
+            "context": checkpoint["context"],
+            "workspace": self._restore_workspace(checkpoint["workspace_state"]),
+            "metadata": checkpoint["metadata"]
+        }
+
+    def _capture_workspace(self, workspace: str) -> dict:
+        """Capture relevant workspace state"""
+        # Git status, file hashes, etc.
+        return {
+            "git_ref": subprocess.getoutput(f"cd {workspace} && git rev-parse HEAD"),
+            "git_dirty": subprocess.getoutput(f"cd {workspace} && git status --porcelain")
+        }
+```
+
+---
+
+## 6. MCP (Model Context Protocol) Integration
+
+### 6.1 MCP Server Pattern
+
+```python
+from mcp import Server, Tool
+
+class MCPAgent:
+    """
+    Agent that can dynamically discover and use MCP tools.
+    'Add a tool that...' pattern from Cline.
+    """
+
+    def __init__(self, llm):
+        self.llm = llm
+        self.mcp_servers = {}
+        self.available_tools = {}
+
+    def connect_server(self, name: str, config: dict) -> None:
+        """Connect to an MCP server"""
+        server = Server(config)
+        self.mcp_servers[name] = server
+
+        # Discover tools
+        tools = server.list_tools()
+        for tool in tools:
+            self.available_tools[tool.name] = {
+                "server": name,
+                "schema": tool.schema
+            }
+
+    async def create_tool(self, description: str) -> str:
+        """
+        Create a new MCP server based on user description.
+        'Add a tool that fetches Jira tickets'
+        """
+        # Generate MCP server code
+        code = self.llm.generate(f"""
+        Create a Python MCP server with a tool that does:
+        {description}
+
+        Use the FastMCP framework. Include proper error handling.
+        Return only the Python code.
+        """)
+
+        # Save and install
+        server_name = self._extract_name(description)
+        path = f"./mcp_servers/{server_name}/server.py"
+
+        with open(path, 'w') as f:
+            f.write(code)
+
+        # Hot-reload
+        self.connect_server(server_name, {"path": path})
+
+        return f"Created tool: {server_name}"
+```
+
+---
+
+## Best Practices Checklist
+
+### Agent Design
+
+- [ ] Clear task decomposition
+- [ ] Appropriate tool granularity
+- [ ] Error handling at each step
+- [ ] Progress visibility to user
+
+### Safety
+
+- [ ] Permission system implemented
+- [ ] Dangerous operations blocked
+- [ ] Sandbox for untrusted code
+- [ ] Audit logging enabled
+
+### UX
+
+- [ ] Approval UI is clear
+- [ ] Progress updates provided
+- [ ] Undo/rollback available
+- [ ] Explanation of actions
+
+---
+
+## Resources
+
+- [Cline](https://github.com/cline/cline)
+- [OpenAI Codex](https://github.com/openai/codex)
+- [Model Context Protocol](https://modelcontextprotocol.io/)
+- [Anthropic Tool Use](https://docs.anthropic.com/claude/docs/tool-use)