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/config.py

@@ -42,7 +42,8 @@ class Settings(BaseSettings):
     working_context_max_items: int = 20
 
     # --- MCP ---
-    mcp_server_command: str = ""
+    mcp_config_path: str = ""  # Path to mcp.json; empty = legacy single-server mode
+    mcp_server_command: str = ""  # Legacy: single server command
     mcp_server_args: list[str] = Field(default_factory=list)
     mcp_timeout_seconds: float = 30.0
     mcp_startup_timeout_seconds: float = 10.0