To add any custom javascript to all the pages, you should create a new custom jsfrag file. The file needs to be deployed in: codebase\netmarkets\javascript\util\jsfrags

The file can be named custom.jsfrag or any other name that is not already in use.

To include the file in all pages run the combine command. This will make the js available in main.js: Windchill/bin>ant -f jsfrag_combine.xml

To add any custom css scripts to all the pages, modify the netmarkets.presentation.cssFiles property in site.xconf to have the necessary css files included. You can include multiple css files as a comma or semicolon separated list in the value. Note that order is important, and that the files will be loaded after the Windchill style sheets so they will properly override the default styles.