Specify custom JS file and Site Logo for a site definition

Scenario:
You want to include a custom JavaScript file, CSS file or a custom logo for your new site definition.

Solution:
Site Definition core file ( ONET.xml ) has top level Project node which supports 'AlternateCSS' , 'CustomJSUrl' and 'SiteLogoUrl' , so use them. make sure you package the required JS and Logo files along with the site definition.

Snippet from ONET.xml:

<Project Title="Company Site Defintion"
Revision="1" ListDir="Lists" AlternateCSS= "/_layouts/Client/custom.css"
CustomJSUrl="/_layouts/Client/custom.js"
SiteLogoUrl="/_layouts/Client/Images/ClientLogo.gif" >

Article:
http://msdn.microsoft.com/en-us/library/ms438080.aspx