Refactor core and reorganize files + add initial docs

README.md

@@ -65,17 +65,25 @@ SimpleAgent is organized in a modular structure:
 ```
 SimpleAgent/
 ├── core/                     # Core framework components
-│   ├── agent.py             # Main SimpleAgent class
-│   ├── run_manager.py       # Execution loop management
-│   ├── execution.py         # Command execution and step management
-│   ├── tool_manager.py      # Dynamic tool loading system
-│   ├── conversation.py      # Conversation history management
-│   ├── memory.py            # Persistent memory system
-│   ├── security.py          # Security and path validation
-│   ├── loop_detector.py     # Loop detection and breaking
-│   ├── summarizer.py        # Change summarization
-│   ├── config.py            # Configuration management
-│   └── version.py           # Version and changelog tracking
+│   ├── agent/               # Agent interface and run loop
+│   │   ├── agent.py         # Main SimpleAgent class
+│   │   └── run_manager.py   # Execution loop management
+│   ├── execution/           # Command execution and tool management
+│   │   ├── execution.py     # Command execution and step management
+│   │   ├── tool_manager.py  # Dynamic tool loading system
+│   │   └── summarizer.py    # Change summarization
+│   ├── conversation/        # Conversation and memory management
+│   │   ├── conversation.py  # Conversation history management
+│   │   └── memory.py        # Persistent memory system
+│   ├── metacognition/       # Metacognition, prompts, and loop detection
+│   │   ├── metacognition.py # Internal monologue and reflection
+│   │   ├── loop_detector.py # Loop detection and breaking
+│   │   └── prompts.py       # Centralized prompt templates
+│   ├── utils/               # Utilities and configuration
+│   │   ├── security.py      # Security and path validation
+│   │   ├── config.py        # Configuration management
+│   │   └── version.py       # Version and changelog tracking
+│   └── __init__.py          # Core package exports
 ├── commands/                 # Local command modules (optional)
 │   └── __init__.py          # Command registration system
 ├── output/                   # Generated files and session data

SimpleAgent/SimpleAgent.py

@@ -25,9 +25,9 @@
 from commands import REGISTERED_COMMANDS, COMMAND_SCHEMAS
 
 # Import core modules
-from core.agent import SimpleAgent
-from core.config import OPENAI_API_KEY, MAX_STEPS, API_PROVIDER, API_BASE_URL, GEMINI_API_KEY, create_client
-from core.version import AGENT_VERSION
+from core.agent.agent import SimpleAgent
+from core.utils.config import OPENAI_API_KEY, MAX_STEPS, API_PROVIDER, API_BASE_URL, GEMINI_API_KEY, create_client
+from core.utils.version import AGENT_VERSION
 
 # Commands will be initialized in main() based on user preference
 

SimpleAgent/commands/__init__.py

@@ -4,12 +4,12 @@
 This package contains all the commands that SimpleAgent can execute.
 Commands are organized by category in subdirectories.
 
-This module now uses the new ToolManager from core.tool_manager to handle
+This module now uses the new ToolManager from core.execution.tool_manager to handle
 both local and remote (GitHub) tools with dynamic loading support.
 """
 
 # Import the new tool manager
-from core.tool_manager import (
+from core.execution.tool_manager import (
     REGISTERED_COMMANDS,
     COMMAND_SCHEMAS,
     register_command,

SimpleAgent/core/__init__.py

@@ -4,13 +4,13 @@
 This package contains the core components of the SimpleAgent system.
 """
 
-from core.agent import SimpleAgent
-from core.summarizer import ChangeSummarizer
-from core.conversation import ConversationManager
-from core.execution import ExecutionManager
-from core.memory import MemoryManager
-from core.run_manager import RunManager
-from core.security import get_secure_path
+from core.agent.agent import SimpleAgent
+from core.execution.summarizer import ChangeSummarizer
+from core.conversation.conversation import ConversationManager
+from core.execution.execution import ExecutionManager
+from core.conversation.memory import MemoryManager
+from core.agent.run_manager import RunManager
+from core.utils.security import get_secure_path
 
 __all__ = [
     "SimpleAgent", 

SimpleAgent/core/agent/__init__.py

@@ -0,0 +1 @@
+

SimpleAgent/core/agent.py → SimpleAgent/core/agent/agent.py

@@ -14,12 +14,12 @@
 import os
 from typing import List, Dict, Any, Optional
 
-from core.conversation import ConversationManager
-from core.execution import ExecutionManager
-from core.memory import MemoryManager
-from core.run_manager import RunManager
-from core.security import get_secure_path
-from core.config import DEFAULT_MODEL, OUTPUT_DIR
+from core.conversation.conversation import ConversationManager
+from core.execution.execution import ExecutionManager
+from core.conversation.memory import MemoryManager
+from core.agent.run_manager import RunManager
+from core.utils.security import get_secure_path
+from core.utils.config import DEFAULT_MODEL, OUTPUT_DIR
 
 
 class SimpleAgent:

SimpleAgent/core/run_manager.py → SimpleAgent/core/agent/run_manager.py

@@ -13,14 +13,14 @@
 import json
 from typing import List, Dict, Any, Optional
 
-from core.conversation import ConversationManager
-from core.execution import ExecutionManager
-from core.memory import MemoryManager
-from core.summarizer import ChangeSummarizer
-from core.loop_detector import LoopDetector
-from core.metacognition import MetaCognition
-from core.prompts import prompts
-from core.config import OUTPUT_DIR
+from core.conversation.conversation import ConversationManager
+from core.execution.execution import ExecutionManager
+from core.conversation.memory import MemoryManager
+from core.execution.summarizer import ChangeSummarizer
+from core.metacognition.loop_detector import LoopDetector
+from core.metacognition.metacognition import MetaCognition
+from core.metacognition.prompts import prompts
+from core.utils.config import OUTPUT_DIR
 
 
 class RunManager:

SimpleAgent/core/conversation/__init__.py

@@ -0,0 +1 @@
+

SimpleAgent/core/memory.py → SimpleAgent/core/conversation/memory.py

@@ -9,7 +9,7 @@
 import json
 from typing import Dict, Any, List
 
-from core.config import MEMORY_FILE, OUTPUT_DIR
+from core.utils.config import MEMORY_FILE, OUTPUT_DIR
 
 
 class MemoryManager:

SimpleAgent/core/execution/__init__.py

@@ -0,0 +1 @@
+

SimpleAgent/core/execution.py → SimpleAgent/core/execution/execution.py

@@ -10,9 +10,9 @@
 import inspect
 from typing import Dict, Any, List, Optional, Tuple, Callable
 
-from core.tool_manager import REGISTERED_COMMANDS, COMMAND_SCHEMAS, load_tool
-from core.security import get_secure_path
-from core.config import OUTPUT_DIR, DEFAULT_MODEL, create_client, API_PROVIDER
+from core.execution.tool_manager import REGISTERED_COMMANDS, COMMAND_SCHEMAS, load_tool
+from core.utils.security import get_secure_path
+from core.utils.config import OUTPUT_DIR, DEFAULT_MODEL, create_client, API_PROVIDER
 
 
 class ExecutionManager:

SimpleAgent/core/summarizer.py → SimpleAgent/core/execution/summarizer.py

@@ -7,7 +7,7 @@
 
 import os
 from typing import List, Dict, Any
-from core.config import SUMMARIZER_MODEL, create_client
+from core.utils.config import SUMMARIZER_MODEL, create_client
 
 
 class ChangeSummarizer:

SimpleAgent/core/tool_manager.py → SimpleAgent/core/execution/tool_manager.py

@@ -24,9 +24,10 @@
 from dataclasses import dataclass, field
 import ast
 import re
+import pathlib
 
 # Import GitHub token from config
-from core.config import GITHUB_TOKEN
+from core.utils.config import GITHUB_TOKEN
 
 # Global registries
 REGISTERED_COMMANDS: Dict[str, Callable] = {}
@@ -72,6 +73,7 @@ def initialize(self) -> None:
         """Initialize the tool manager by discovering available tools."""
         self.logger.info("🚀 Initializing Tool Manager...")
         self._create_temp_directory()
+        self._discover_local_tools()
         self._discover_tools()
         self._register_tool_schemas()
         self.logger.info(f"✅ Discovered {len(self.tools)} tools")
@@ -82,6 +84,35 @@ def _create_temp_directory(self) -> None:
         # Add to Python path
         sys.path.insert(0, self.temp_dir)
 
+    def _discover_local_tools(self):
+        """Discover all available tools from the local commands directory."""
+        base_dir = pathlib.Path(__file__).parent.parent / 'commands'
+        if not base_dir.exists():
+            return
+        for category_dir in base_dir.iterdir():
+            if not category_dir.is_dir() or category_dir.name.startswith('__'):
+                continue
+            for tool_dir in category_dir.iterdir():
+                if not tool_dir.is_dir() or tool_dir.name.startswith('__'):
+                    continue
+                init_file = tool_dir / '__init__.py'
+                if not init_file.exists():
+                    continue
+                module_name = f"commands.{category_dir.name}.{tool_dir.name}"
+                if module_name in sys.modules:
+                    continue
+                try:
+                    importlib.import_module(module_name)
+                    tool = Tool(
+                        name=tool_dir.name,
+                        category=category_dir.name,
+                        github_path=None
+                    )
+                    self.tools[tool_dir.name] = tool
+                    self.logger.debug(f"Discovered local tool: {tool_dir.name} in {category_dir.name}")
+                except Exception as e:
+                    self.logger.error(f"Failed to import local tool {module_name}: {e}")
+
     def _discover_tools(self) -> None:
         """Discover all available tools from GitHub repository."""
         try:

SimpleAgent/core/metacognition/__init__.py

@@ -0,0 +1 @@
+

SimpleAgent/core/loop_detector.py → SimpleAgent/core/metacognition/loop_detector.py

@@ -16,7 +16,7 @@ class LoopDetector:
     to help break out of unproductive patterns.
 
     Loop breaking messages are generated by the centralized prompt system
-    in core.prompts for better maintainability. Use generate_breaking_message()
+    in core.metacognition.prompts for better maintainability. Use generate_breaking_message()
     to create intervention messages.
     """
 
@@ -175,7 +175,7 @@ def generate_breaking_message(self, loop_info: Dict[str, Any], original_instruct
                 conversation_manager.add_message("user", message)
         """
         # Import here to avoid circular imports
-        from core.prompts import prompts
+        from core.metacognition.prompts import prompts
 
         return prompts.format_loop_breaking_message(
             loop_type=loop_info['type'],