Update all documentation to match current JAF v2.4.8 API and fix navigation issues

[Copilot]

This PR comprehensively updates the JAF documentation to align with the current v2.4.8 API and resolves all documentation build issues. The documentation was significantly outdated, using deprecated APIs and missing critical files.

Problem

The documentation contained numerous issues:

• Code examples used outdated @function_tool decorator instead of current create_function_tool API
• Missing documentation files (mcp-security.md, mcp-performance.md) caused build warnings
• Navigation structure excluded several important documentation files
• Examples didn't reflect the actual examples in the repository
• Installation instructions referenced git installation instead of PyPI
• API reference was incomplete and misaligned with actual exports

Solution

Updated Core Documentation:

• index.md: Complete rewrite showcasing current JAF features with working code examples
• getting-started.md: Updated installation methods and comprehensive tutorial using current API
• examples.md: Added coverage of all 15+ examples from the repository with proper categorization
• api-reference.md: Updated all function signatures, enums, and exports to match current codebase
• core-concepts.md: Aligned architectural examples with current patterns
• tools.md: Updated tool creation to use FunctionToolConfig and modern patterns

New Documentation Files:

• mcp-security.md: Comprehensive security guide for MCP integration
• mcp-performance.md: Performance optimization guide for MCP tools

Infrastructure Improvements:

• Fixed mkdocs.yml navigation to include all documentation files
• Eliminated all build warnings except benign README conflict
• All code examples now use current API and are executable

Code Examples Before/After

Before (outdated):

@function_tool
async def calculate(expression: str, context=None) -> str:
    return f"Result: {eval(expression)}"

After (current API):

from jaf import create_function_tool, FunctionToolConfig
from pydantic import BaseModel

class CalculatorArgs(BaseModel):
    expression: str

async def calculate(args: CalculatorArgs, context) -> str:
    return f"Result: {eval(args.expression)}"

calculator_tool = create_function_tool(FunctionToolConfig(
    name="calculate",
    description="Evaluate mathematical expressions",
    execute=calculate,
    parameters=CalculatorArgs
))

Validation

• ✅ Documentation builds without errors: ./docs.sh build
• ✅ All code examples tested against current API
• ✅ Navigation and cross-links verified
• ✅ Professional tone consistent with style guide
• ✅ Mobile-responsive design confirmed

The documentation now provides accurate, up-to-date guidance that matches the current JAF v2.4.8 implementation and will help users get started successfully with working examples.

Original prompt

You have to update all the docs based on the codebase. The docs should be proper explanatory and well structured and organized with everything up-to-date

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