gistfile1.js

jQuery( function () {
	My_Object.init( params );
} );

(function ( $, app ) {
	/**
	 * A variable
	 */
	 app.var = 42;
	 
	/**
	 * Bootstrap
	 */
	app.init = function( params ) {

		// Do stuff
	};
	
	/**
	 * Another function
	 */
	app.another_function = function( params ) {
		//do more stuff
	};
	

})( jQuery, window.My_Object || ( window.My_Object = {} ) );

gistfile2.js

jQuery( function () {
	My_Object.init( params );
} );

(function ( $, app ) {
	/**
	 * A variable
	 */
	 app.var = 42;
	 
	/**
	 * Bootstrap
	 */
	app.init = function( params ) {

		// Do stuff
	};
	
	/**
	 * Another function
	 */
	app.another_function = function( params ) {
		//do more stuff
	};
	
	app.events.clickHandler = function() {
		//something
	}
	
	app.events.formSubmitHandler = function() {
		//something
	}
	

})( jQuery, window.My_Object || ( window.My_Object = {} ) );