Add .gitignore, remove __pycache__ from tracking, and update MCP/orchestrator modules

- Add .gitignore to exclude .env, __pycache__, node_modules, and IDE files
- Remove all __pycache__ bytecode files from version control
- Add MCP config files (mcp.json, mcp.json.example)
- Add MCP manager, registry, and config modules
- Update routes, orchestrator engine, and agent base with latest changes

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

src/orchestrator/engine.py

@@ -13,7 +13,7 @@ from typing import Any
 from ..adapters.base import ModelAdapter
 from ..config import settings
 from ..context.engine import ContextEngine
-from ..mcp.client import MCPClient
+from ..mcp.manager import MCPManager
 from ..memory.store import MemoryStore
 from ..models.agent import AgentRole
 from ..models.session import SessionState, SessionStatus, TaskStatus
@@ -34,7 +34,7 @@ class OrchestratorEngine:
         self,
         model_adapter: ModelAdapter,
         context_engine: ContextEngine,
-        mcp_client: MCPClient,
+        mcp_client: MCPManager,
         memory_store: MemoryStore,
         sse_emitter: SSEEmitter,
     ) -> None: