Reorganize: Move all skills to skills/ folder

- Created skills/ directory
- Moved 272 skills to skills/ subfolder
- Kept agents/ at root level
- Kept installation scripts and docs at root level

Repository structure:
- skills/           - All 272 skills from skills.sh
- agents/           - Agent definitions
- *.sh, *.ps1       - Installation scripts
- README.md, etc.   - Documentation

Co-Authored-By: Claude <noreply@anthropic.com>

skills/brainstorming/.agent/workspace/phase2-research.md

@@ -0,0 +1,67 @@
+# Phase 2: Terminal Execution Enhancements - Research Document
+
+## Research Summary
+
+### Modular Tool System Architecture
+
+Based on research of leading AI agent frameworks (AutoGen, Xaibo, ReAct patterns), here are key architectural patterns:
+
+#### 1. Tool Abstraction Layer
+```python
+# Base tool interface
+class Tool:
+    name: str
+    description: str
+    parameters: dict
+
+    async def execute(self, **kwargs) -> ToolResult:
+        pass
+```
+
+#### 2. Tool Registry Pattern
+```python
+class ToolRegistry:
+    def register(self, tool: Tool)
+    def get(self, name: str) -> Tool
+    def list_available(self) -> List[Tool]
+    def execute(self, tool_name: str, **kwargs) -> ToolResult
+```
+
+#### 3. ReAct Pattern Integration
+- **Thought**: Agent reasoning about what to do
+- **Action**: Selecting and executing a tool
+- **Observation**: Result from tool execution
+- **Iteration**: Loop until completion
+
+#### 4. Key Features from Research
+- **Xaibo**: Tool providers make Python functions available as tools
+- **AutoGen**: Built-in `PythonCodeExecutionTool` with custom agent support
+- **ReAct**: `agent_loop()` controller that parses reasoning and executes tools
+- **Temporal**: Durable agents that evaluate available tools
+
+### Implementation Plan for Phase 2
+
+#### Task 2.1: Create Modular Tool System
+1. **Base Tool Interface** - Abstract class for all tools
+2. **Concrete Tool Implementations**:
+   - `ShellTool` - Execute shell commands
+   - `FileOperationTool` - File system operations
+   - `WebSearchTool` - Web search capabilities
+   - `CodeExecutionTool` - Python code execution
+
+#### Task 2.2: Enhanced Intent Analysis
+1. **Command Classification** - Better detection of command types
+2. **Tool Selection** - Automatic tool selection based on intent
+3. **Context Awareness** - Remember previous commands for suggestions
+
+#### Task 2.3: Error Handling & Output Formatting
+1. **Structured Error Responses** - Clear, actionable error messages
+2. **Output Formatting** - Rich output with syntax highlighting
+3. **Telemetry** - Track command success rates and patterns
+
+## Sources
+- [Xaibo - Modular AI Agent Framework](https://xaibo.ai/tutorial/getting-started/)
+- [Microsoft AutoGen Framework](https://github.com/microsoft/autogen)
+- [AutoGen Tools Documentation](https://microsoft.github.io/autogen/stable//user-guide/core-user-guide/components/tools.html)
+- [ReAct Pattern Implementation](https://til.simonwillison.net/llms/python-react-pattern)
+- [Multi-Agent Design Patterns](https://medium.com/aimonks/multi-agent-system-design-patterns-from-scratch-in-python-react-agents-e4480d099f38)